Starting phenix.real_space_refine on Mon Mar 18 23:37:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua1_26412/03_2024/7ua1_26412_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua1_26412/03_2024/7ua1_26412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua1_26412/03_2024/7ua1_26412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua1_26412/03_2024/7ua1_26412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua1_26412/03_2024/7ua1_26412_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ua1_26412/03_2024/7ua1_26412_neut_updated.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 940 5.16 5 C 88268 2.51 5 N 23588 2.21 5 O 25856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2790": "OE1" <-> "OE2" Residue "A PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2790": "OE1" <-> "OE2" Residue "B PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2790": "OE1" <-> "OE2" Residue "C PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2790": "OE1" <-> "OE2" Residue "D PHE 3162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4750": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.39s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138680 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34480 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34480 Chain: "C" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34480 Chain: "D" Number of atoms: 33766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33758 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34480 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 1, 'ATP': 2, 'KVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33087 SG CYS A4888 168.960 194.432 124.639 1.00 86.88 S ATOM 33112 SG CYS A4891 169.306 191.937 121.743 1.00 87.07 S ATOM 70125 SG CYS B4888 194.437 199.009 124.641 1.00 87.49 S ATOM 70150 SG CYS B4891 191.943 198.666 121.744 1.00 87.20 S ATOM A0303 SG CYS C4888 199.030 173.544 124.632 1.00 87.13 S ATOM A030S SG CYS C4891 198.685 176.040 121.737 1.00 86.99 S ATOM A0T21 SG CYS D4888 173.572 168.973 124.655 1.00 87.35 S ATOM A0T2Q SG CYS D4891 176.066 169.318 121.758 1.00 87.40 S Time building chain proxies: 90.00, per 1000 atoms: 0.65 Number of scatterers: 138680 At special positions: 0 Unit cell: (369.408, 369.408, 212.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 940 16.00 P 24 15.00 O 25856 8.00 N 23588 7.00 C 88268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " distance=2.03 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 40.31 Conformation dependent library (CDL) restraints added in 34.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 8 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 696 helices and 76 sheets defined 58.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 43.57 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 5.635A pdb=" N SER A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.786A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.251A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 5.293A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 5.446A pdb=" N THR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 removed outlier: 4.138A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 4.697A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.888A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 4.810A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.370A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 557 through 563' Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.671A pdb=" N ILE A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.632A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.619A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.758A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE A 862 " --> pdb=" O THR A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 862' Processing helix chain 'A' and resid 881 through 900 Processing helix chain 'A' and resid 920 through 947 removed outlier: 3.744A pdb=" N LEU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix removed outlier: 6.420A pdb=" N GLU A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 4.555A pdb=" N ASP A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 5.318A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.989A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1226 through 1231 removed outlier: 3.563A pdb=" N CYS A1230 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A1231 " --> pdb=" O PHE A1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1226 through 1231' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 4.016A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 4.400A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.861A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.142A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.605A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.690A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 3.737A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 3.541A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR A1737 " --> pdb=" O THR A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1803 Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.626A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 4.012A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1955 Processing helix chain 'A' and resid 1958 through 1967 removed outlier: 3.857A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A1967 " --> pdb=" O LYS A1963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1978 Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 4.528A pdb=" N GLN A1995 " --> pdb=" O GLU A1991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.731A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.999A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.345A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.827A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.963A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.047A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2258 removed outlier: 5.613A pdb=" N ARG A2258 " --> pdb=" O ALA A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2275 Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.594A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2332 through 2337 removed outlier: 3.944A pdb=" N ARG A2336 " --> pdb=" O GLY A2332 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY A2337 " --> pdb=" O PRO A2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2332 through 2337' Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.972A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A2468 " --> pdb=" O HIS A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2503 removed outlier: 3.832A pdb=" N LEU A2502 " --> pdb=" O ALA A2498 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 4.233A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 3.531A pdb=" N ARG A2518 " --> pdb=" O LEU A2514 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 3.791A pdb=" N SER A2547 " --> pdb=" O SER A2543 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.605A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.140A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2618 removed outlier: 4.446A pdb=" N LEU A2607 " --> pdb=" O ALA A2603 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A2618 " --> pdb=" O TYR A2614 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.302A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2677 removed outlier: 3.758A pdb=" N LEU A2666 " --> pdb=" O PHE A2662 " (cutoff:3.500A) Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 removed outlier: 4.450A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP A2696 " --> pdb=" O GLN A2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2691 through 2696' Processing helix chain 'A' and resid 2717 through 2740 Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.604A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2786 removed outlier: 4.977A pdb=" N GLU A2769 " --> pdb=" O GLU A2765 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 3.592A pdb=" N GLY A2786 " --> pdb=" O MET A2782 " (cutoff:3.500A) Processing helix chain 'A' and resid 2794 through 2802 removed outlier: 6.251A pdb=" N MET A2798 " --> pdb=" O GLU A2794 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A2799 " --> pdb=" O GLY A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.432A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 5.374A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2947 Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 5.326A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.773A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3078 removed outlier: 5.254A pdb=" N GLN A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.275A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3117 through 3122 Processing helix chain 'A' and resid 3124 through 3143 Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 3.672A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3188 through 3196 removed outlier: 4.357A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 4.871A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3224 removed outlier: 5.127A pdb=" N ALA A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A3223 " --> pdb=" O VAL A3219 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 4.138A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 5.192A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 Proline residue: A3258 - end of helix Processing helix chain 'A' and resid 3269 through 3288 Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.742A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.844A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3318 removed outlier: 5.136A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3332 removed outlier: 4.829A pdb=" N THR A3332 " --> pdb=" O LYS A3328 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3606 removed outlier: 5.718A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3613 through 3628 Processing helix chain 'A' and resid 3636 through 3646 Processing helix chain 'A' and resid 3649 through 3654 Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.702A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.180A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.563A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.527A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.802A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3959 removed outlier: 3.662A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4036 removed outlier: 3.574A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP A4030 " --> pdb=" O LEU A4026 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A4031 " --> pdb=" O THR A4027 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A4032 " --> pdb=" O SER A4028 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A4033 " --> pdb=" O SER A4029 " (cutoff:3.500A) Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.124A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.129A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 4.087A pdb=" N ASP A4093 " --> pdb=" O GLU A4089 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY A4095 " --> pdb=" O ALA A4091 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A4096 " --> pdb=" O LYS A4092 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.611A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4130 Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4208 removed outlier: 5.349A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4261 removed outlier: 4.632A pdb=" N LEU A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4272 Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 3.707A pdb=" N TYR A4287 " --> pdb=" O PHE A4283 " (cutoff:3.500A) Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 4.299A pdb=" N ILE A4484 " --> pdb=" O PHE A4480 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 4.419A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4568 through 4612 removed outlier: 4.121A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.521A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4675 through 4683 Processing helix chain 'A' and resid 4695 through 4701 removed outlier: 4.058A pdb=" N SER A4700 " --> pdb=" O ALA A4696 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.713A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4749 removed outlier: 4.696A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4750 through 4762 removed outlier: 3.872A pdb=" N SER A4759 " --> pdb=" O THR A4755 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.342A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.169A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.240A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 removed outlier: 3.990A pdb=" N MET A4884 " --> pdb=" O VAL A4880 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS A4887 " --> pdb=" O ASP A4883 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 3.839A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A4900 " --> pdb=" O ASP A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 5.655A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR A1776 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1772 through 1778' Processing helix chain 'A' and resid 4614 through 4619 removed outlier: 3.625A pdb=" N GLU A4619 " --> pdb=" O GLY A4614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4614 through 4619' Processing helix chain 'B' and resid 51 through 56 removed outlier: 5.636A pdb=" N SER B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.786A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.251A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 5.293A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 438 removed outlier: 4.138A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 4.697A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.888A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 removed outlier: 4.810A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.370A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 563' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.671A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.631A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.619A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.758A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 862 " --> pdb=" O THR B 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 857 through 862' Processing helix chain 'B' and resid 881 through 900 Processing helix chain 'B' and resid 920 through 947 removed outlier: 3.744A pdb=" N LEU B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Proline residue: B 925 - end of helix removed outlier: 6.420A pdb=" N GLU B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 4.555A pdb=" N ASP B 959 " --> pdb=" O GLU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 5.318A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.989A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1226 through 1231 removed outlier: 3.564A pdb=" N CYS B1230 " --> pdb=" O TYR B1226 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B1231 " --> pdb=" O PHE B1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1226 through 1231' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 4.017A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 4.400A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.860A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.143A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.606A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.690A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 3.737A pdb=" N MET B1721 " --> pdb=" O ALA B1717 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1737 removed outlier: 3.541A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR B1737 " --> pdb=" O THR B1733 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1803 Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.626A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 4.013A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1955 Processing helix chain 'B' and resid 1958 through 1967 removed outlier: 3.857A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER B1967 " --> pdb=" O LYS B1963 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1978 Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 4.528A pdb=" N GLN B1995 " --> pdb=" O GLU B1991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.732A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.999A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.346A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.826A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.963A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.048A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2258 removed outlier: 5.614A pdb=" N ARG B2258 " --> pdb=" O ALA B2254 " (cutoff:3.500A) Processing helix chain 'B' and resid 2259 through 2275 Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.593A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2332 through 2337 removed outlier: 3.945A pdb=" N ARG B2336 " --> pdb=" O GLY B2332 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY B2337 " --> pdb=" O PRO B2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2332 through 2337' Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.971A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B2468 " --> pdb=" O HIS B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2503 removed outlier: 3.832A pdb=" N LEU B2502 " --> pdb=" O ALA B2498 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 4.233A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 3.531A pdb=" N ARG B2518 " --> pdb=" O LEU B2514 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 3.790A pdb=" N SER B2547 " --> pdb=" O SER B2543 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.606A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.139A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2603 through 2618 removed outlier: 4.446A pdb=" N LEU B2607 " --> pdb=" O ALA B2603 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B2618 " --> pdb=" O TYR B2614 " (cutoff:3.500A) Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.302A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2658 through 2677 removed outlier: 3.757A pdb=" N LEU B2666 " --> pdb=" O PHE B2662 " (cutoff:3.500A) Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 removed outlier: 4.451A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP B2696 " --> pdb=" O GLN B2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2691 through 2696' Processing helix chain 'B' and resid 2717 through 2740 Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.605A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 4.977A pdb=" N GLU B2769 " --> pdb=" O GLU B2765 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 3.592A pdb=" N GLY B2786 " --> pdb=" O MET B2782 " (cutoff:3.500A) Processing helix chain 'B' and resid 2794 through 2802 removed outlier: 6.253A pdb=" N MET B2798 " --> pdb=" O GLU B2794 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B2799 " --> pdb=" O GLY B2795 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.431A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 5.373A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2947 Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 5.326A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.772A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3078 removed outlier: 5.253A pdb=" N GLN B3077 " --> pdb=" O GLU B3073 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.275A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3117 through 3122 Processing helix chain 'B' and resid 3124 through 3143 Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 3.671A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3188 through 3196 removed outlier: 4.358A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 4.870A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3224 removed outlier: 5.128A pdb=" N ALA B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B3223 " --> pdb=" O VAL B3219 " (cutoff:3.500A) Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 4.139A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 5.192A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 Proline residue: B3258 - end of helix Processing helix chain 'B' and resid 3269 through 3288 Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.741A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.845A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3318 removed outlier: 5.136A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) Processing helix chain 'B' and resid 3319 through 3332 removed outlier: 4.829A pdb=" N THR B3332 " --> pdb=" O LYS B3328 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3606 removed outlier: 5.718A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3613 through 3628 Processing helix chain 'B' and resid 3636 through 3646 Processing helix chain 'B' and resid 3649 through 3654 Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.702A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.180A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.563A pdb=" N CYS B3847 " --> pdb=" O LEU B3843 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.527A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.801A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3959 removed outlier: 3.662A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4036 removed outlier: 3.573A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP B4030 " --> pdb=" O LEU B4026 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B4031 " --> pdb=" O THR B4027 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE B4032 " --> pdb=" O SER B4028 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS B4033 " --> pdb=" O SER B4029 " (cutoff:3.500A) Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.124A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.130A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 4.087A pdb=" N ASP B4093 " --> pdb=" O GLU B4089 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY B4095 " --> pdb=" O ALA B4091 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B4096 " --> pdb=" O LYS B4092 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.611A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4130 Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4208 removed outlier: 5.349A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4261 removed outlier: 4.632A pdb=" N LEU B4261 " --> pdb=" O ARG B4257 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4272 Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 3.707A pdb=" N TYR B4287 " --> pdb=" O PHE B4283 " (cutoff:3.500A) Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 4.299A pdb=" N ILE B4484 " --> pdb=" O PHE B4480 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 4.419A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4612 removed outlier: 4.122A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.522A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4675 through 4683 Processing helix chain 'B' and resid 4695 through 4701 removed outlier: 4.059A pdb=" N SER B4700 " --> pdb=" O ALA B4696 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.713A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4749 removed outlier: 4.695A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) Processing helix chain 'B' and resid 4750 through 4762 removed outlier: 3.873A pdb=" N SER B4759 " --> pdb=" O THR B4755 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.341A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.169A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.240A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 removed outlier: 3.991A pdb=" N MET B4884 " --> pdb=" O VAL B4880 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS B4887 " --> pdb=" O ASP B4883 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 3.840A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B4900 " --> pdb=" O ASP B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 5.655A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR B1776 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1772 through 1778' Processing helix chain 'B' and resid 4614 through 4619 removed outlier: 3.623A pdb=" N GLU B4619 " --> pdb=" O GLY B4614 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4614 through 4619' Processing helix chain 'C' and resid 51 through 56 removed outlier: 5.635A pdb=" N SER C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.786A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 253 through 258 removed outlier: 4.251A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 5.293A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 438 removed outlier: 4.138A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.698A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.888A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 removed outlier: 4.811A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.370A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 563' Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.670A pdb=" N ILE C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 Processing helix chain 'C' and resid 607 through 619 removed outlier: 3.632A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.619A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.758A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE C 862 " --> pdb=" O THR C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 862' Processing helix chain 'C' and resid 881 through 900 Processing helix chain 'C' and resid 920 through 947 removed outlier: 3.744A pdb=" N LEU C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Proline residue: C 925 - end of helix removed outlier: 6.419A pdb=" N GLU C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 961 removed outlier: 4.555A pdb=" N ASP C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 5.318A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.989A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1226 through 1231 removed outlier: 3.563A pdb=" N CYS C1230 " --> pdb=" O TYR C1226 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C1231 " --> pdb=" O PHE C1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1226 through 1231' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 4.016A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 4.400A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.860A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.143A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.606A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.690A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 3.738A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1737 removed outlier: 3.541A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR C1737 " --> pdb=" O THR C1733 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1803 Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.626A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 4.013A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1950 through 1955 Processing helix chain 'C' and resid 1958 through 1967 removed outlier: 3.858A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C1967 " --> pdb=" O LYS C1963 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1978 Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 4.528A pdb=" N GLN C1995 " --> pdb=" O GLU C1991 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.730A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.999A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.346A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.826A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.963A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.048A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2258 removed outlier: 5.612A pdb=" N ARG C2258 " --> pdb=" O ALA C2254 " (cutoff:3.500A) Processing helix chain 'C' and resid 2259 through 2275 Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.594A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2332 through 2337 removed outlier: 3.945A pdb=" N ARG C2336 " --> pdb=" O GLY C2332 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY C2337 " --> pdb=" O PRO C2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2332 through 2337' Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.971A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET C2468 " --> pdb=" O HIS C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2503 removed outlier: 3.831A pdb=" N LEU C2502 " --> pdb=" O ALA C2498 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 4.233A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 3.531A pdb=" N ARG C2518 " --> pdb=" O LEU C2514 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 3.791A pdb=" N SER C2547 " --> pdb=" O SER C2543 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.606A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.139A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2603 through 2618 removed outlier: 4.446A pdb=" N LEU C2607 " --> pdb=" O ALA C2603 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C2618 " --> pdb=" O TYR C2614 " (cutoff:3.500A) Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.303A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2658 through 2677 removed outlier: 3.757A pdb=" N LEU C2666 " --> pdb=" O PHE C2662 " (cutoff:3.500A) Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 removed outlier: 4.451A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP C2696 " --> pdb=" O GLN C2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2691 through 2696' Processing helix chain 'C' and resid 2717 through 2740 Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.604A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2786 removed outlier: 4.977A pdb=" N GLU C2769 " --> pdb=" O GLU C2765 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 3.591A pdb=" N GLY C2786 " --> pdb=" O MET C2782 " (cutoff:3.500A) Processing helix chain 'C' and resid 2794 through 2802 removed outlier: 6.252A pdb=" N MET C2798 " --> pdb=" O GLU C2794 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA C2799 " --> pdb=" O GLY C2795 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.432A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 5.374A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2947 Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 5.326A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.773A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3078 removed outlier: 5.253A pdb=" N GLN C3077 " --> pdb=" O GLU C3073 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.276A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3117 through 3122 Processing helix chain 'C' and resid 3124 through 3143 Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 3.672A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3188 through 3196 removed outlier: 4.358A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 4.871A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3224 removed outlier: 5.128A pdb=" N ALA C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C3223 " --> pdb=" O VAL C3219 " (cutoff:3.500A) Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 4.139A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 5.193A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 Proline residue: C3258 - end of helix Processing helix chain 'C' and resid 3269 through 3288 Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.741A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.845A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3318 removed outlier: 5.136A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) Processing helix chain 'C' and resid 3319 through 3332 removed outlier: 4.830A pdb=" N THR C3332 " --> pdb=" O LYS C3328 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3606 removed outlier: 5.719A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3613 through 3628 Processing helix chain 'C' and resid 3636 through 3646 Processing helix chain 'C' and resid 3649 through 3654 Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.701A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.181A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.563A pdb=" N CYS C3847 " --> pdb=" O LEU C3843 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.528A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.801A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3959 removed outlier: 3.662A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4036 removed outlier: 3.573A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP C4030 " --> pdb=" O LEU C4026 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C4031 " --> pdb=" O THR C4027 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE C4032 " --> pdb=" O SER C4028 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS C4033 " --> pdb=" O SER C4029 " (cutoff:3.500A) Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.124A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.130A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 4.087A pdb=" N ASP C4093 " --> pdb=" O GLU C4089 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY C4095 " --> pdb=" O ALA C4091 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C4096 " --> pdb=" O LYS C4092 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.611A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4130 Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4208 removed outlier: 5.350A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4261 removed outlier: 4.633A pdb=" N LEU C4261 " --> pdb=" O ARG C4257 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4272 Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 3.706A pdb=" N TYR C4287 " --> pdb=" O PHE C4283 " (cutoff:3.500A) Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 4.299A pdb=" N ILE C4484 " --> pdb=" O PHE C4480 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 4.419A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4568 through 4612 removed outlier: 4.121A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.522A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4675 through 4683 Processing helix chain 'C' and resid 4695 through 4701 removed outlier: 4.059A pdb=" N SER C4700 " --> pdb=" O ALA C4696 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) Processing helix chain 'C' and resid 4702 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.713A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4749 removed outlier: 4.697A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4750 through 4762 removed outlier: 3.873A pdb=" N SER C4759 " --> pdb=" O THR C4755 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.341A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.169A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.240A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 removed outlier: 3.991A pdb=" N MET C4884 " --> pdb=" O VAL C4880 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS C4887 " --> pdb=" O ASP C4883 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 3.840A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C4900 " --> pdb=" O ASP C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 5.655A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR C1776 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1772 through 1778' Processing helix chain 'C' and resid 4614 through 4619 removed outlier: 3.625A pdb=" N GLU C4619 " --> pdb=" O GLY C4614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4614 through 4619' Processing helix chain 'D' and resid 51 through 56 removed outlier: 5.635A pdb=" N SER D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.786A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 253 through 258 removed outlier: 4.250A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 5.293A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 438 removed outlier: 4.138A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 4.697A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.887A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 556 removed outlier: 4.811A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.370A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 563' Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.671A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.632A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.619A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.758A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE D 862 " --> pdb=" O THR D 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 857 through 862' Processing helix chain 'D' and resid 881 through 900 Processing helix chain 'D' and resid 920 through 947 removed outlier: 3.743A pdb=" N LEU D 924 " --> pdb=" O GLU D 920 " (cutoff:3.500A) Proline residue: D 925 - end of helix removed outlier: 6.420A pdb=" N GLU D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 961 removed outlier: 4.555A pdb=" N ASP D 959 " --> pdb=" O GLU D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 5.318A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.989A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1226 through 1231 removed outlier: 3.564A pdb=" N CYS D1230 " --> pdb=" O TYR D1226 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D1231 " --> pdb=" O PHE D1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1226 through 1231' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 4.016A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 4.401A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.861A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.142A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.606A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.690A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 3.738A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1737 removed outlier: 3.540A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR D1737 " --> pdb=" O THR D1733 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1803 Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.626A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 4.013A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1950 through 1955 Processing helix chain 'D' and resid 1958 through 1967 removed outlier: 3.858A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER D1967 " --> pdb=" O LYS D1963 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1978 Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 4.528A pdb=" N GLN D1995 " --> pdb=" O GLU D1991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.730A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.998A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.346A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.827A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.963A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.048A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2258 removed outlier: 5.613A pdb=" N ARG D2258 " --> pdb=" O ALA D2254 " (cutoff:3.500A) Processing helix chain 'D' and resid 2259 through 2275 Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.594A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2332 through 2337 removed outlier: 3.944A pdb=" N ARG D2336 " --> pdb=" O GLY D2332 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY D2337 " --> pdb=" O PRO D2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2332 through 2337' Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.972A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET D2468 " --> pdb=" O HIS D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2503 removed outlier: 3.832A pdb=" N LEU D2502 " --> pdb=" O ALA D2498 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 4.233A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 3.532A pdb=" N ARG D2518 " --> pdb=" O LEU D2514 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 3.791A pdb=" N SER D2547 " --> pdb=" O SER D2543 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.606A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.140A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2603 through 2618 removed outlier: 4.446A pdb=" N LEU D2607 " --> pdb=" O ALA D2603 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP D2618 " --> pdb=" O TYR D2614 " (cutoff:3.500A) Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.302A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2658 through 2677 removed outlier: 3.758A pdb=" N LEU D2666 " --> pdb=" O PHE D2662 " (cutoff:3.500A) Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 removed outlier: 4.451A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP D2696 " --> pdb=" O GLN D2692 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2691 through 2696' Processing helix chain 'D' and resid 2717 through 2740 Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.604A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 4.977A pdb=" N GLU D2769 " --> pdb=" O GLU D2765 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 3.592A pdb=" N GLY D2786 " --> pdb=" O MET D2782 " (cutoff:3.500A) Processing helix chain 'D' and resid 2794 through 2802 removed outlier: 6.251A pdb=" N MET D2798 " --> pdb=" O GLU D2794 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA D2799 " --> pdb=" O GLY D2795 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.431A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 5.374A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2947 Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 5.327A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.773A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3078 removed outlier: 5.253A pdb=" N GLN D3077 " --> pdb=" O GLU D3073 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.276A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3117 through 3122 Processing helix chain 'D' and resid 3124 through 3143 Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 3.672A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3188 through 3196 removed outlier: 4.357A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 4.871A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3224 removed outlier: 5.128A pdb=" N ALA D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D3223 " --> pdb=" O VAL D3219 " (cutoff:3.500A) Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 4.139A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 5.192A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 Proline residue: D3258 - end of helix Processing helix chain 'D' and resid 3269 through 3288 Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.741A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.845A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3318 removed outlier: 5.136A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) Processing helix chain 'D' and resid 3319 through 3332 removed outlier: 4.829A pdb=" N THR D3332 " --> pdb=" O LYS D3328 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3606 removed outlier: 5.718A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3613 through 3628 Processing helix chain 'D' and resid 3636 through 3646 Processing helix chain 'D' and resid 3649 through 3654 Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.702A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.180A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.562A pdb=" N CYS D3847 " --> pdb=" O LEU D3843 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.527A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.801A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3959 removed outlier: 3.661A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4036 removed outlier: 3.573A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP D4030 " --> pdb=" O LEU D4026 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D4031 " --> pdb=" O THR D4027 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE D4032 " --> pdb=" O SER D4028 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS D4033 " --> pdb=" O SER D4029 " (cutoff:3.500A) Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.124A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.129A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 4.087A pdb=" N ASP D4093 " --> pdb=" O GLU D4089 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY D4095 " --> pdb=" O ALA D4091 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE D4096 " --> pdb=" O LYS D4092 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.611A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4130 Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4208 removed outlier: 5.349A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4261 removed outlier: 4.632A pdb=" N LEU D4261 " --> pdb=" O ARG D4257 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4272 Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 3.706A pdb=" N TYR D4287 " --> pdb=" O PHE D4283 " (cutoff:3.500A) Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 4.300A pdb=" N ILE D4484 " --> pdb=" O PHE D4480 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 4.418A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4612 removed outlier: 4.121A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.522A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4675 through 4683 Processing helix chain 'D' and resid 4695 through 4701 removed outlier: 4.059A pdb=" N SER D4700 " --> pdb=" O ALA D4696 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) Processing helix chain 'D' and resid 4702 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.713A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4749 removed outlier: 4.696A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4750 through 4762 removed outlier: 3.873A pdb=" N SER D4759 " --> pdb=" O THR D4755 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.342A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.168A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.240A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 removed outlier: 3.991A pdb=" N MET D4884 " --> pdb=" O VAL D4880 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS D4887 " --> pdb=" O ASP D4883 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 3.840A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D4900 " --> pdb=" O ASP D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 5.654A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR D1776 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1772 through 1778' Processing helix chain 'D' and resid 4614 through 4619 removed outlier: 3.624A pdb=" N GLU D4619 " --> pdb=" O GLY D4614 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4614 through 4619' Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.631A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 3.627A pdb=" N MET E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.631A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 3.627A pdb=" N MET F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.630A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.627A pdb=" N MET G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.631A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 3.627A pdb=" N MET H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 5.258A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.441A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.531A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 192 through 196 Processing sheet with id= 4, first strand: chain 'A' and resid 243 through 246 removed outlier: 5.768A pdb=" N VAL A 260 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY A 264 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE A 387 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 313 through 318 removed outlier: 3.613A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 14.177A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.569A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 765 through 769 removed outlier: 3.679A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 9, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.409A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 948 through 952 removed outlier: 4.109A pdb=" N GLU A1065 " --> pdb=" O HIS A 949 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 6.277A pdb=" N GLN A1021 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1142 through 1145 removed outlier: 3.797A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1257 through 1260 removed outlier: 4.796A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 6.733A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 2443 through 2446 Processing sheet with id= 16, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 17, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.787A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 19, first strand: chain 'B' and resid 47 through 50 removed outlier: 5.257A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.442A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.531A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 192 through 196 Processing sheet with id= 22, first strand: chain 'B' and resid 243 through 246 removed outlier: 5.767A pdb=" N VAL B 260 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B 264 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B 387 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.612A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 14.177A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.568A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 765 through 769 removed outlier: 3.679A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 27, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.410A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 948 through 952 removed outlier: 4.110A pdb=" N GLU B1065 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 6.277A pdb=" N GLN B1021 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 1142 through 1145 removed outlier: 3.797A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1257 through 1260 removed outlier: 4.796A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 6.733A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 2443 through 2446 Processing sheet with id= 34, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 35, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.787A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 37, first strand: chain 'C' and resid 47 through 50 removed outlier: 5.257A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.442A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.531A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 192 through 196 Processing sheet with id= 40, first strand: chain 'C' and resid 243 through 246 removed outlier: 5.767A pdb=" N VAL C 260 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY C 264 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE C 387 " --> pdb=" O GLY C 264 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 313 through 318 removed outlier: 3.612A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 14.176A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.568A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 765 through 769 removed outlier: 3.679A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 45, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.409A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 948 through 952 removed outlier: 4.110A pdb=" N GLU C1065 " --> pdb=" O HIS C 949 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 6.277A pdb=" N GLN C1021 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 1142 through 1145 removed outlier: 3.796A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 1257 through 1260 removed outlier: 4.797A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 6.732A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 2443 through 2446 Processing sheet with id= 52, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 53, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.787A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 55, first strand: chain 'D' and resid 47 through 50 removed outlier: 5.257A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.442A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.530A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 192 through 196 Processing sheet with id= 58, first strand: chain 'D' and resid 243 through 246 removed outlier: 5.767A pdb=" N VAL D 260 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY D 264 " --> pdb=" O ILE D 387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE D 387 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 313 through 318 removed outlier: 3.612A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 14.177A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 693 through 697 removed outlier: 3.569A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 765 through 769 removed outlier: 3.679A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 63, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.409A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 948 through 952 removed outlier: 4.110A pdb=" N GLU D1065 " --> pdb=" O HIS D 949 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 6.277A pdb=" N GLN D1021 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 1142 through 1145 removed outlier: 3.797A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 1257 through 1260 removed outlier: 4.797A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 6.733A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 2443 through 2446 Processing sheet with id= 70, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 71, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.787A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 73, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.605A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLN E 21 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.605A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLN F 21 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.605A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLN G 21 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.605A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLN H 21 " --> pdb=" O ILE H 51 " (cutoff:3.500A) 7336 hydrogen bonds defined for protein. 21916 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: 110.54 Time building geometry restraints manager: 44.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 45410 1.34 - 1.47: 32833 1.47 - 1.59: 61915 1.59 - 1.71: 30 1.71 - 1.83: 1520 Bond restraints: 141708 Sorted by residual: bond pdb=" C4 ATP A5003 " pdb=" C5 ATP A5003 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" C5 ATP A5003 " pdb=" C6 ATP A5003 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 bond pdb=" C5 ATP A5003 " pdb=" N7 ATP A5003 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" C8 ATP A5003 " pdb=" N7 ATP A5003 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.80e+01 bond pdb=" C4 ATP A5003 " pdb=" N9 ATP A5003 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.57e+01 ... (remaining 141703 not shown) Histogram of bond angle deviations from ideal: 97.11 - 105.67: 2899 105.67 - 114.22: 82565 114.22 - 122.78: 94461 122.78 - 131.33: 11273 131.33 - 139.89: 270 Bond angle restraints: 191468 Sorted by residual: angle pdb=" PA ATP A5003 " pdb=" O3A ATP A5003 " pdb=" PB ATP A5003 " ideal model delta sigma weight residual 136.83 119.59 17.24 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PB ATP A5003 " pdb=" O3B ATP A5003 " pdb=" PG ATP A5003 " ideal model delta sigma weight residual 139.87 122.64 17.23 1.00e+00 1.00e+00 2.97e+02 angle pdb=" C5 ATP A5003 " pdb=" C4 ATP A5003 " pdb=" N3 ATP A5003 " ideal model delta sigma weight residual 126.80 118.03 8.77 1.00e+00 1.00e+00 7.70e+01 angle pdb=" N3 ATP A5003 " pdb=" C4 ATP A5003 " pdb=" N9 ATP A5003 " ideal model delta sigma weight residual 127.04 136.10 -9.06 1.15e+00 7.59e-01 6.23e+01 angle pdb=" CA ARG B1960 " pdb=" CB ARG B1960 " pdb=" CG ARG B1960 " ideal model delta sigma weight residual 114.10 128.50 -14.40 2.00e+00 2.50e-01 5.18e+01 ... (remaining 191463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 83648 34.50 - 69.00: 1596 69.00 - 103.50: 220 103.50 - 138.00: 5 138.00 - 172.50: 7 Dihedral angle restraints: 85476 sinusoidal: 35116 harmonic: 50360 Sorted by residual: dihedral pdb=" CA LYS B3187 " pdb=" C LYS B3187 " pdb=" N SER B3188 " pdb=" CA SER B3188 " ideal model delta harmonic sigma weight residual 180.00 132.93 47.07 0 5.00e+00 4.00e-02 8.86e+01 dihedral pdb=" CA LYS A3187 " pdb=" C LYS A3187 " pdb=" N SER A3188 " pdb=" CA SER A3188 " ideal model delta harmonic sigma weight residual 180.00 132.94 47.06 0 5.00e+00 4.00e-02 8.86e+01 dihedral pdb=" CA LYS D3187 " pdb=" C LYS D3187 " pdb=" N SER D3188 " pdb=" CA SER D3188 " ideal model delta harmonic sigma weight residual 180.00 132.95 47.05 0 5.00e+00 4.00e-02 8.86e+01 ... (remaining 85473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 15996 0.043 - 0.086: 3844 0.086 - 0.128: 1040 0.128 - 0.171: 86 0.171 - 0.214: 22 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB VAL B2176 " pdb=" CA VAL B2176 " pdb=" CG1 VAL B2176 " pdb=" CG2 VAL B2176 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL D2176 " pdb=" CA VAL D2176 " pdb=" CG1 VAL D2176 " pdb=" CG2 VAL D2176 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A2176 " pdb=" CA VAL A2176 " pdb=" CG1 VAL A2176 " pdb=" CG2 VAL A2176 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 20985 not shown) Planarity restraints: 24596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D2914 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO D2915 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D2915 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D2915 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C2914 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO C2915 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C2915 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C2915 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B2914 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B2915 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B2915 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B2915 " -0.036 5.00e-02 4.00e+02 ... (remaining 24593 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 318 2.41 - 3.03: 83804 3.03 - 3.65: 216751 3.65 - 4.28: 324018 4.28 - 4.90: 534618 Nonbonded interactions: 1159509 Sorted by model distance: nonbonded pdb=" NE ARG A1011 " pdb=" O2G ATP A5003 " model vdw 1.785 2.496 nonbonded pdb=" O LEU A1957 " pdb=" NH1 ARG A1960 " model vdw 2.106 2.520 nonbonded pdb=" O LEU B1957 " pdb=" NH1 ARG B1960 " model vdw 2.106 2.520 nonbonded pdb=" O LEU D1957 " pdb=" NH1 ARG D1960 " model vdw 2.106 2.520 nonbonded pdb=" O LEU C1957 " pdb=" NH1 ARG C1960 " model vdw 2.107 2.520 ... (remaining 1159504 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' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.390 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: 0.140 Extract box with map and model: 30.750 Check model and map are aligned: 1.470 Set scattering table: 0.920 Process input model: 449.690 Find NCS groups from input model: 7.620 Set up NCS constraints: 1.060 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: 0.030 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 509.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 0.077 141708 Z= 0.183 Angle : 0.619 17.243 191468 Z= 0.328 Chirality : 0.040 0.214 20988 Planarity : 0.004 0.096 24596 Dihedral : 14.480 172.500 53000 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.32 % Favored : 96.56 % Rotamer: Outliers : 0.29 % Allowed : 0.28 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.20 (0.07), residues: 17212 helix: 1.89 (0.06), residues: 8928 sheet: 0.06 (0.13), residues: 1656 loop : -0.49 (0.08), residues: 6628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1156 HIS 0.013 0.001 HIS H 26 PHE 0.036 0.001 PHE A4048 TYR 0.020 0.001 TYR C4520 ARG 0.018 0.000 ARG A1051 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1070 time to evaluate : 11.899 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: A 931 TYR cc_start: 0.8319 (m-10) cc_final: 0.7991 (m-80) REVERT: A 1035 TYR cc_start: 0.7314 (t80) cc_final: 0.6844 (t80) REVERT: A 3235 MET cc_start: 0.7479 (pmm) cc_final: 0.6898 (ppp) REVERT: A 3319 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: A 4060 GLN cc_start: 0.8496 (tp40) cc_final: 0.8283 (tp40) REVERT: A 4558 HIS cc_start: 0.7234 (m-70) cc_final: 0.6928 (m-70) REVERT: A 4707 MET cc_start: 0.8362 (ttt) cc_final: 0.8097 (ttp) REVERT: E 58 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7769 (ptmm) REVERT: F 3 VAL cc_start: 0.8345 (t) cc_final: 0.8125 (t) REVERT: F 58 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7530 (ptmm) REVERT: G 18 LYS cc_start: 0.8954 (mppt) cc_final: 0.8745 (mppt) REVERT: G 51 ILE cc_start: 0.9203 (tp) cc_final: 0.8948 (OUTLIER) REVERT: G 61 GLU cc_start: 0.8055 (tp30) cc_final: 0.7754 (mm-30) REVERT: H 51 ILE cc_start: 0.9246 (tp) cc_final: 0.8946 (tp) REVERT: B 1035 TYR cc_start: 0.7079 (t80) cc_final: 0.6746 (t80) REVERT: B 2468 MET cc_start: 0.7953 (mmp) cc_final: 0.7726 (mmt) REVERT: B 2710 ASN cc_start: 0.7433 (p0) cc_final: 0.7212 (p0) REVERT: B 3121 LEU cc_start: 0.8827 (tt) cc_final: 0.8485 (tp) REVERT: B 3235 MET cc_start: 0.7604 (pmm) cc_final: 0.7121 (ppp) REVERT: B 3241 MET cc_start: 0.7310 (tmm) cc_final: 0.7040 (tmm) REVERT: B 3246 MET cc_start: 0.8610 (mtt) cc_final: 0.8356 (mtm) REVERT: B 3319 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: B 3904 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7445 (mtm110) REVERT: B 3954 MET cc_start: 0.7903 (mmm) cc_final: 0.7257 (mtm) REVERT: C 1035 TYR cc_start: 0.7160 (t80) cc_final: 0.6777 (t80) REVERT: C 2468 MET cc_start: 0.7970 (mmp) cc_final: 0.7760 (mmt) REVERT: C 3130 CYS cc_start: 0.8381 (m) cc_final: 0.7694 (m) REVERT: C 3214 LEU cc_start: 0.9244 (mp) cc_final: 0.9038 (mp) REVERT: C 3235 MET cc_start: 0.7620 (pmm) cc_final: 0.7179 (ppp) REVERT: C 3241 MET cc_start: 0.7815 (tmm) cc_final: 0.7539 (tmm) REVERT: C 3246 MET cc_start: 0.8884 (mtt) cc_final: 0.8668 (mtp) REVERT: C 3279 ASN cc_start: 0.8275 (m110) cc_final: 0.7769 (t0) REVERT: C 3319 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: D 934 GLN cc_start: 0.8409 (pp30) cc_final: 0.8131 (pp30) REVERT: D 1035 TYR cc_start: 0.7329 (t80) cc_final: 0.6914 (t80) REVERT: D 3130 CYS cc_start: 0.8365 (m) cc_final: 0.7789 (m) REVERT: D 3180 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8953 (pp) REVERT: D 3235 MET cc_start: 0.7425 (pmm) cc_final: 0.7193 (ppp) REVERT: D 3319 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: D 4002 MET cc_start: 0.8650 (tmm) cc_final: 0.8446 (tmm) outliers start: 44 outliers final: 4 residues processed: 1086 average time/residue: 2.0603 time to fit residues: 3202.1544 Evaluate side-chains 913 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 904 time to evaluate : 11.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3072 MET Chi-restraints excluded: chain A residue 3319 PHE Chi-restraints excluded: chain B residue 3072 MET Chi-restraints excluded: chain B residue 3319 PHE Chi-restraints excluded: chain B residue 3904 ARG Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 3319 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3319 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 6.9990 chunk 1309 optimal weight: 9.9990 chunk 726 optimal weight: 7.9990 chunk 447 optimal weight: 10.0000 chunk 883 optimal weight: 1.9990 chunk 699 optimal weight: 0.9990 chunk 1354 optimal weight: 4.9990 chunk 524 optimal weight: 10.0000 chunk 823 optimal weight: 9.9990 chunk 1008 optimal weight: 9.9990 chunk 1569 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2639 HIS A2704 GLN A3279 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN F 44 ASN G 44 ASN H 44 ASN H 95 ASN B 12 GLN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 ASN B2386 ASN B2639 HIS B2704 GLN ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 150 GLN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2639 HIS C2704 GLN C2838 HIS A C2838 HIS B ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2639 HIS D2704 GLN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3279 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 141708 Z= 0.349 Angle : 0.649 14.103 191468 Z= 0.329 Chirality : 0.043 0.289 20988 Planarity : 0.005 0.080 24596 Dihedral : 7.092 161.979 19126 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 0.76 % Allowed : 5.97 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.07 (0.06), residues: 17212 helix: 1.81 (0.06), residues: 8900 sheet: -0.08 (0.13), residues: 1648 loop : -0.56 (0.08), residues: 6664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1156 HIS 0.011 0.002 HIS G 26 PHE 0.028 0.002 PHE D3170 TYR 0.033 0.002 TYR D2801 ARG 0.015 0.001 ARG B1013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 993 time to evaluate : 10.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 892 LEU cc_start: 0.8571 (mp) cc_final: 0.8196 (pt) REVERT: A 895 MET cc_start: 0.8983 (ptt) cc_final: 0.8619 (ppp) REVERT: A 964 MET cc_start: -0.1997 (OUTLIER) cc_final: -0.2450 (pmm) REVERT: A 1035 TYR cc_start: 0.7433 (t80) cc_final: 0.6881 (t80) REVERT: A 1051 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7977 (mtt180) REVERT: A 2150 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7901 (mtt) REVERT: A 2688 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5827 (tpp) REVERT: A 2689 MET cc_start: 0.5316 (tmm) cc_final: 0.4600 (tpp) REVERT: A 2732 TRP cc_start: 0.7869 (t60) cc_final: 0.7609 (t60) REVERT: A 2956 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: A 2958 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7599 (tp40) REVERT: A 3235 MET cc_start: 0.7492 (pmm) cc_final: 0.7056 (ppp) REVERT: A 3315 LEU cc_start: 0.9182 (mm) cc_final: 0.8835 (mm) REVERT: A 4048 PHE cc_start: 0.8920 (t80) cc_final: 0.8686 (t80) REVERT: A 4060 GLN cc_start: 0.8615 (tp40) cc_final: 0.8386 (tp40) REVERT: A 4558 HIS cc_start: 0.7387 (m-70) cc_final: 0.7078 (m-70) REVERT: A 4748 MET cc_start: 0.7150 (mpt) cc_final: 0.6883 (mpt) REVERT: E 30 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7247 (mtp) REVERT: G 61 GLU cc_start: 0.8035 (tp30) cc_final: 0.7670 (tt0) REVERT: B 964 MET cc_start: -0.1974 (OUTLIER) cc_final: -0.2364 (pmm) REVERT: B 1035 TYR cc_start: 0.7161 (t80) cc_final: 0.6732 (t80) REVERT: B 1165 MET cc_start: 0.8429 (mpp) cc_final: 0.8189 (mtm) REVERT: B 3121 LEU cc_start: 0.8872 (tt) cc_final: 0.8506 (tp) REVERT: B 3235 MET cc_start: 0.7594 (pmm) cc_final: 0.7187 (ppp) REVERT: B 3241 MET cc_start: 0.7609 (tmm) cc_final: 0.7243 (tmm) REVERT: B 3246 MET cc_start: 0.8705 (mtt) cc_final: 0.8421 (mtm) REVERT: B 3315 LEU cc_start: 0.9167 (mm) cc_final: 0.8853 (mm) REVERT: B 4660 PHE cc_start: 0.7490 (p90) cc_final: 0.7261 (p90) REVERT: C 895 MET cc_start: 0.8685 (ptt) cc_final: 0.8343 (ppp) REVERT: C 964 MET cc_start: -0.1901 (OUTLIER) cc_final: -0.2390 (pmm) REVERT: C 1031 ARG cc_start: 0.7751 (ttt-90) cc_final: 0.7309 (mmm160) REVERT: C 1035 TYR cc_start: 0.7178 (t80) cc_final: 0.6756 (t80) REVERT: C 1051 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7967 (mtt180) REVERT: C 2956 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: C 3121 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 3130 CYS cc_start: 0.8411 (m) cc_final: 0.7654 (m) REVERT: C 3214 LEU cc_start: 0.9240 (mp) cc_final: 0.9027 (mp) REVERT: C 3235 MET cc_start: 0.7569 (pmm) cc_final: 0.7136 (ppp) REVERT: C 3241 MET cc_start: 0.7864 (tmm) cc_final: 0.7484 (tmm) REVERT: C 3279 ASN cc_start: 0.8588 (m110) cc_final: 0.8307 (m110) REVERT: C 3302 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7805 (t80) REVERT: C 3315 LEU cc_start: 0.9166 (mm) cc_final: 0.8944 (mm) REVERT: C 3981 MET cc_start: 0.8690 (tmm) cc_final: 0.8426 (tmt) REVERT: C 4048 PHE cc_start: 0.8670 (t80) cc_final: 0.8458 (t80) REVERT: C 4268 MET cc_start: 0.2203 (tmt) cc_final: 0.1475 (ptm) REVERT: C 4558 HIS cc_start: 0.7440 (m90) cc_final: 0.7159 (m-70) REVERT: D 1035 TYR cc_start: 0.7290 (t80) cc_final: 0.6764 (t80) REVERT: D 1051 ARG cc_start: 0.8384 (mtm180) cc_final: 0.7976 (mtt180) REVERT: D 1165 MET cc_start: 0.8392 (mpp) cc_final: 0.8173 (mtm) REVERT: D 2468 MET cc_start: 0.8065 (mmp) cc_final: 0.7540 (mmt) REVERT: D 2793 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6671 (mmm160) REVERT: D 3220 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8140 (mp0) REVERT: D 3235 MET cc_start: 0.7446 (pmm) cc_final: 0.6997 (ppp) REVERT: D 3315 LEU cc_start: 0.9315 (mm) cc_final: 0.8981 (mm) REVERT: D 3797 MET cc_start: 0.8678 (mtt) cc_final: 0.8473 (mtt) REVERT: D 4048 PHE cc_start: 0.8820 (t80) cc_final: 0.8599 (t80) REVERT: D 4558 HIS cc_start: 0.7543 (m90) cc_final: 0.7316 (m-70) REVERT: D 4660 PHE cc_start: 0.7755 (p90) cc_final: 0.7106 (p90) REVERT: D 4943 MET cc_start: 0.8734 (mtp) cc_final: 0.8531 (mtp) outliers start: 114 outliers final: 16 residues processed: 1017 average time/residue: 2.0800 time to fit residues: 3033.5284 Evaluate side-chains 953 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 927 time to evaluate : 11.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 1948 MET Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2173 GLU Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2722 ASN Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3302 PHE Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 3166 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 4.9990 chunk 487 optimal weight: 9.9990 chunk 1306 optimal weight: 10.0000 chunk 1068 optimal weight: 6.9990 chunk 432 optimal weight: 6.9990 chunk 1572 optimal weight: 9.9990 chunk 1698 optimal weight: 10.0000 chunk 1400 optimal weight: 0.9990 chunk 1558 optimal weight: 9.9990 chunk 535 optimal weight: 8.9990 chunk 1261 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A2838 HIS A A2838 HIS B ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3279 ASN A3882 GLN A3955 GLN A3975 GLN A4049 HIS A4933 HIS E 26 HIS F 26 HIS F 44 ASN G 26 HIS G 44 ASN H 26 HIS B 150 GLN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2838 HIS B ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3279 ASN B3955 GLN B3975 GLN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4060 GLN B4088 HIS B4178 ASN B4558 HIS B4933 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 ASN ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3257 ASN C3634 HIS C3949 HIS C3955 GLN C3975 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4178 ASN D 150 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 HIS D 781 ASN D2802 ASN D2838 HIS A ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3882 GLN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4178 ASN D4933 HIS ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 141708 Z= 0.460 Angle : 0.663 17.316 191468 Z= 0.335 Chirality : 0.044 0.308 20988 Planarity : 0.005 0.080 24596 Dihedral : 6.613 119.348 19106 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.06 % Rotamer: Outliers : 0.94 % Allowed : 7.50 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.06), residues: 17212 helix: 1.70 (0.06), residues: 8952 sheet: -0.28 (0.13), residues: 1672 loop : -0.68 (0.08), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C3250 HIS 0.013 0.002 HIS E 26 PHE 0.038 0.002 PHE C4660 TYR 0.043 0.002 TYR A2801 ARG 0.014 0.001 ARG B1051 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 962 time to evaluate : 12.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 964 MET cc_start: -0.1500 (mpt) cc_final: -0.2000 (pmm) REVERT: A 1035 TYR cc_start: 0.7577 (t80) cc_final: 0.7044 (t80) REVERT: A 1050 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8822 (tp) REVERT: A 2689 MET cc_start: 0.5408 (tmm) cc_final: 0.4604 (pmm) REVERT: A 2732 TRP cc_start: 0.7870 (t60) cc_final: 0.7620 (t60) REVERT: A 2958 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7669 (tp40) REVERT: A 3319 PHE cc_start: 0.8406 (m-80) cc_final: 0.7561 (m-80) REVERT: A 3689 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: A 3854 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8292 (t80) REVERT: A 4048 PHE cc_start: 0.8933 (t80) cc_final: 0.8576 (t80) REVERT: A 4060 GLN cc_start: 0.8614 (tp40) cc_final: 0.8388 (tp40) REVERT: A 4558 HIS cc_start: 0.7490 (m-70) cc_final: 0.7238 (m90) REVERT: A 4748 MET cc_start: 0.7336 (mpt) cc_final: 0.7024 (mpt) REVERT: E 30 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7308 (mtp) REVERT: G 61 GLU cc_start: 0.8039 (tp30) cc_final: 0.7662 (tt0) REVERT: B 895 MET cc_start: 0.8911 (ptt) cc_final: 0.8530 (ppp) REVERT: B 964 MET cc_start: -0.1509 (mpt) cc_final: -0.1957 (pmm) REVERT: B 1035 TYR cc_start: 0.7297 (t80) cc_final: 0.6908 (t80) REVERT: B 1051 ARG cc_start: 0.8343 (mtm110) cc_final: 0.8092 (mtm180) REVERT: B 1165 MET cc_start: 0.8487 (mpp) cc_final: 0.8276 (mtm) REVERT: B 2173 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: B 2939 TYR cc_start: 0.8161 (m-80) cc_final: 0.7790 (m-80) REVERT: B 3121 LEU cc_start: 0.8888 (tt) cc_final: 0.8530 (tp) REVERT: B 3235 MET cc_start: 0.7663 (pmm) cc_final: 0.7319 (pp-130) REVERT: B 3241 MET cc_start: 0.7690 (tmm) cc_final: 0.7317 (tmm) REVERT: B 3315 LEU cc_start: 0.9199 (mm) cc_final: 0.8894 (mm) REVERT: B 3854 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8339 (t80) REVERT: B 4502 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7628 (mtm) REVERT: B 4660 PHE cc_start: 0.8192 (p90) cc_final: 0.7988 (p90) REVERT: C 895 MET cc_start: 0.8774 (ptt) cc_final: 0.8405 (ppp) REVERT: C 934 GLN cc_start: 0.8560 (pp30) cc_final: 0.8265 (pp30) REVERT: C 964 MET cc_start: -0.2108 (mpt) cc_final: -0.2476 (pmm) REVERT: C 1031 ARG cc_start: 0.7852 (ttt-90) cc_final: 0.7282 (mmm160) REVERT: C 1035 TYR cc_start: 0.7336 (t80) cc_final: 0.6913 (t80) REVERT: C 1051 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7885 (mtt180) REVERT: C 2734 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6683 (mpt) REVERT: C 3130 CYS cc_start: 0.8431 (m) cc_final: 0.7695 (m) REVERT: C 3214 LEU cc_start: 0.9269 (mp) cc_final: 0.9010 (mp) REVERT: C 3220 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 3241 MET cc_start: 0.7984 (tmm) cc_final: 0.7641 (tmm) REVERT: C 3315 LEU cc_start: 0.9129 (mm) cc_final: 0.8929 (mm) REVERT: C 3319 PHE cc_start: 0.8525 (m-80) cc_final: 0.7902 (m-80) REVERT: C 3689 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7613 (mpp) REVERT: C 3854 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8295 (t80) REVERT: C 3981 MET cc_start: 0.8658 (tmm) cc_final: 0.8404 (tmt) REVERT: C 4048 PHE cc_start: 0.8765 (t80) cc_final: 0.8375 (t80) REVERT: C 4246 PHE cc_start: 0.8188 (t80) cc_final: 0.7694 (t80) REVERT: C 4558 HIS cc_start: 0.7446 (m90) cc_final: 0.7151 (m-70) REVERT: D 128 MET cc_start: 0.8796 (mtt) cc_final: 0.8543 (mtp) REVERT: D 565 LEU cc_start: 0.8788 (tp) cc_final: 0.8588 (tm) REVERT: D 895 MET cc_start: 0.8699 (ptt) cc_final: 0.8182 (ppp) REVERT: D 934 GLN cc_start: 0.8479 (pp30) cc_final: 0.8182 (pp30) REVERT: D 1031 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7160 (mmm160) REVERT: D 1035 TYR cc_start: 0.7561 (t80) cc_final: 0.7020 (t80) REVERT: D 2798 MET cc_start: 0.6114 (tpt) cc_final: 0.5509 (tpt) REVERT: D 3130 CYS cc_start: 0.8431 (m) cc_final: 0.7984 (m) REVERT: D 3219 VAL cc_start: 0.9355 (t) cc_final: 0.9100 (t) REVERT: D 3220 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8353 (mp0) REVERT: D 3241 MET cc_start: 0.7914 (tmm) cc_final: 0.7697 (tmm) REVERT: D 3302 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7853 (t80) REVERT: D 4048 PHE cc_start: 0.8812 (t80) cc_final: 0.8536 (t80) REVERT: D 4558 HIS cc_start: 0.7484 (m90) cc_final: 0.7201 (m-70) outliers start: 136 outliers final: 34 residues processed: 1007 average time/residue: 2.0045 time to fit residues: 2912.2639 Evaluate side-chains 966 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 921 time to evaluate : 11.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 3680 CYS Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 931 TYR Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 1948 MET Chi-restraints excluded: chain B residue 2173 GLU Chi-restraints excluded: chain B residue 2688 MET Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3279 ASN Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4558 HIS Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 2389 MET Chi-restraints excluded: chain C residue 2722 ASN Chi-restraints excluded: chain C residue 2734 MET Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3147 TYR Chi-restraints excluded: chain C residue 3166 PHE Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 2770 ILE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3302 PHE Chi-restraints excluded: chain D residue 3680 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 8.9990 chunk 1181 optimal weight: 20.0000 chunk 815 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 750 optimal weight: 9.9990 chunk 1055 optimal weight: 9.9990 chunk 1577 optimal weight: 10.0000 chunk 1670 optimal weight: 6.9990 chunk 824 optimal weight: 2.9990 chunk 1495 optimal weight: 1.9990 chunk 450 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 HIS ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3279 ASN A3955 GLN A3975 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS E 44 ASN F 26 HIS F 44 ASN G 26 HIS G 44 ASN H 26 HIS B 150 GLN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2838 HIS A ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3955 GLN B3975 GLN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4558 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS C3882 GLN C3955 GLN C3975 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4088 HIS D 12 GLN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2838 HIS B ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 141708 Z= 0.402 Angle : 0.633 14.438 191468 Z= 0.320 Chirality : 0.043 0.451 20988 Planarity : 0.005 0.068 24596 Dihedral : 6.436 118.783 19106 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 0.95 % Allowed : 8.48 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.06), residues: 17212 helix: 1.78 (0.06), residues: 8900 sheet: -0.27 (0.13), residues: 1692 loop : -0.68 (0.08), residues: 6620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B2732 HIS 0.021 0.001 HIS B4558 PHE 0.031 0.002 PHE A4016 TYR 0.048 0.002 TYR A 931 ARG 0.014 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 946 time to evaluate : 11.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 892 LEU cc_start: 0.8725 (mp) cc_final: 0.8291 (pt) REVERT: A 895 MET cc_start: 0.8875 (ptt) cc_final: 0.8376 (ppp) REVERT: A 964 MET cc_start: -0.1606 (mpt) cc_final: -0.2102 (pmm) REVERT: A 1035 TYR cc_start: 0.7556 (t80) cc_final: 0.7042 (t80) REVERT: A 2689 MET cc_start: 0.5169 (tmm) cc_final: 0.4364 (pmm) REVERT: A 2732 TRP cc_start: 0.7831 (t60) cc_final: 0.7563 (t60) REVERT: A 2793 ARG cc_start: 0.7370 (mmm160) cc_final: 0.6714 (mmm160) REVERT: A 2958 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7649 (tp40) REVERT: A 3235 MET cc_start: 0.7537 (pmm) cc_final: 0.6913 (ppp) REVERT: A 3246 MET cc_start: 0.8899 (mtp) cc_final: 0.8594 (mtt) REVERT: A 3315 LEU cc_start: 0.9200 (mm) cc_final: 0.8951 (mm) REVERT: A 3319 PHE cc_start: 0.8087 (m-80) cc_final: 0.7766 (m-80) REVERT: A 3854 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8262 (t80) REVERT: A 4048 PHE cc_start: 0.8937 (t80) cc_final: 0.8660 (t80) REVERT: A 4060 GLN cc_start: 0.8590 (tp40) cc_final: 0.8368 (tp40) REVERT: A 4502 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7695 (mtm) REVERT: A 4558 HIS cc_start: 0.7544 (m-70) cc_final: 0.7298 (m90) REVERT: E 30 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7283 (mtp) REVERT: G 61 GLU cc_start: 0.8066 (tp30) cc_final: 0.7710 (tt0) REVERT: B 895 MET cc_start: 0.8918 (ptt) cc_final: 0.8612 (ppp) REVERT: B 933 LEU cc_start: 0.9014 (tm) cc_final: 0.8679 (tm) REVERT: B 964 MET cc_start: -0.1756 (mpt) cc_final: -0.2158 (pmm) REVERT: B 1035 TYR cc_start: 0.7328 (t80) cc_final: 0.6907 (t80) REVERT: B 1051 ARG cc_start: 0.8314 (mtm110) cc_final: 0.8103 (mtm180) REVERT: B 1165 MET cc_start: 0.8455 (mpp) cc_final: 0.8169 (mtm) REVERT: B 2173 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: B 3121 LEU cc_start: 0.8888 (tt) cc_final: 0.8529 (tp) REVERT: B 3235 MET cc_start: 0.7645 (pmm) cc_final: 0.7325 (pp-130) REVERT: B 3241 MET cc_start: 0.7776 (tmm) cc_final: 0.7448 (tmm) REVERT: B 3315 LEU cc_start: 0.9258 (mm) cc_final: 0.9013 (mm) REVERT: B 3689 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7714 (mpp) REVERT: B 3854 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8354 (t80) REVERT: B 3904 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7623 (mtm-85) REVERT: B 3954 MET cc_start: 0.8262 (mmm) cc_final: 0.7491 (mtm) REVERT: B 4660 PHE cc_start: 0.8148 (p90) cc_final: 0.7948 (p90) REVERT: C 469 HIS cc_start: 0.8453 (p90) cc_final: 0.8105 (p90) REVERT: C 895 MET cc_start: 0.8837 (ptt) cc_final: 0.8493 (ppp) REVERT: C 934 GLN cc_start: 0.8553 (pp30) cc_final: 0.8250 (pp30) REVERT: C 964 MET cc_start: -0.2111 (mpt) cc_final: -0.2519 (pmm) REVERT: C 1031 ARG cc_start: 0.7825 (ttt-90) cc_final: 0.6972 (mtp-110) REVERT: C 1035 TYR cc_start: 0.7307 (t80) cc_final: 0.6863 (t80) REVERT: C 1051 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7902 (mtt180) REVERT: C 1477 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7647 (m-70) REVERT: C 3130 CYS cc_start: 0.8468 (m) cc_final: 0.8042 (m) REVERT: C 3214 LEU cc_start: 0.9268 (mp) cc_final: 0.9010 (mp) REVERT: C 3220 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8393 (mm-30) REVERT: C 3235 MET cc_start: 0.7495 (pmm) cc_final: 0.6793 (ppp) REVERT: C 3241 MET cc_start: 0.8017 (tmm) cc_final: 0.7600 (tmm) REVERT: C 3279 ASN cc_start: 0.8648 (m110) cc_final: 0.8388 (m110) REVERT: C 3854 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8324 (t80) REVERT: C 3981 MET cc_start: 0.8666 (tmm) cc_final: 0.8414 (tmt) REVERT: C 4048 PHE cc_start: 0.8744 (t80) cc_final: 0.8295 (t80) REVERT: C 4246 PHE cc_start: 0.8175 (t80) cc_final: 0.7669 (t80) REVERT: C 4558 HIS cc_start: 0.7492 (m90) cc_final: 0.7220 (m-70) REVERT: D 128 MET cc_start: 0.8765 (mtt) cc_final: 0.8511 (mtp) REVERT: D 895 MET cc_start: 0.8740 (ptt) cc_final: 0.8270 (ppp) REVERT: D 1035 TYR cc_start: 0.7526 (t80) cc_final: 0.7014 (t80) REVERT: D 1051 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7994 (mtm180) REVERT: D 2347 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8200 (mmt) REVERT: D 2512 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7221 (tpp) REVERT: D 2798 MET cc_start: 0.6301 (tpt) cc_final: 0.5578 (tpt) REVERT: D 3130 CYS cc_start: 0.8440 (m) cc_final: 0.7955 (m) REVERT: D 3219 VAL cc_start: 0.9186 (t) cc_final: 0.8714 (p) REVERT: D 3220 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 3235 MET cc_start: 0.7447 (pmm) cc_final: 0.6913 (ppp) REVERT: D 3246 MET cc_start: 0.9012 (mtp) cc_final: 0.8752 (mtp) REVERT: D 3302 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7820 (t80) REVERT: D 3854 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8360 (t80) REVERT: D 3981 MET cc_start: 0.8679 (tmm) cc_final: 0.8441 (tmm) REVERT: D 4048 PHE cc_start: 0.8841 (t80) cc_final: 0.8528 (t80) REVERT: D 4558 HIS cc_start: 0.7531 (m90) cc_final: 0.7239 (m-70) outliers start: 137 outliers final: 29 residues processed: 1016 average time/residue: 2.0209 time to fit residues: 2981.4870 Evaluate side-chains 966 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 925 time to evaluate : 11.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 2722 ASN Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3149 GLU Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 2173 GLU Chi-restraints excluded: chain B residue 2688 MET Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1477 HIS Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2722 ASN Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2512 MET Chi-restraints excluded: chain D residue 2722 ASN Chi-restraints excluded: chain D residue 3149 GLU Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3302 PHE Chi-restraints excluded: chain D residue 3854 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 50.0000 chunk 948 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 1243 optimal weight: 10.0000 chunk 689 optimal weight: 0.9980 chunk 1425 optimal weight: 2.9990 chunk 1154 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 852 optimal weight: 7.9990 chunk 1499 optimal weight: 9.9990 chunk 421 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4088 HIS E 44 ASN F 44 ASN G 44 ASN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 141708 Z= 0.247 Angle : 0.599 17.727 191468 Z= 0.299 Chirality : 0.041 0.360 20988 Planarity : 0.004 0.077 24596 Dihedral : 6.197 117.901 19106 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.05 % Rotamer: Outliers : 0.97 % Allowed : 9.11 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.07), residues: 17212 helix: 1.90 (0.06), residues: 8912 sheet: -0.21 (0.13), residues: 1688 loop : -0.61 (0.08), residues: 6612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D2741 HIS 0.010 0.001 HIS C3700 PHE 0.029 0.001 PHE A4016 TYR 0.053 0.001 TYR A 931 ARG 0.018 0.000 ARG A1051 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 958 time to evaluate : 11.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 892 LEU cc_start: 0.8763 (mp) cc_final: 0.8371 (pt) REVERT: A 895 MET cc_start: 0.8877 (ptt) cc_final: 0.8156 (ppp) REVERT: A 964 MET cc_start: -0.1592 (mpt) cc_final: -0.2087 (pmm) REVERT: A 995 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7814 (mpp) REVERT: A 1035 TYR cc_start: 0.7500 (t80) cc_final: 0.6997 (t80) REVERT: A 1050 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8605 (tp) REVERT: A 1051 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7854 (ptp-170) REVERT: A 1215 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8369 (mtt) REVERT: A 2689 MET cc_start: 0.5051 (tmm) cc_final: 0.4248 (pmm) REVERT: A 2732 TRP cc_start: 0.7846 (t60) cc_final: 0.7612 (t60) REVERT: A 2793 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6634 (mmm160) REVERT: A 2798 MET cc_start: 0.6241 (tpt) cc_final: 0.5615 (tpt) REVERT: A 2958 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7683 (tp40) REVERT: A 3220 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 3235 MET cc_start: 0.7532 (pmm) cc_final: 0.6980 (ppp) REVERT: A 3246 MET cc_start: 0.8838 (mtp) cc_final: 0.8552 (mtt) REVERT: A 3315 LEU cc_start: 0.9219 (mm) cc_final: 0.8985 (mm) REVERT: A 3319 PHE cc_start: 0.8113 (m-80) cc_final: 0.7779 (m-80) REVERT: A 3689 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7364 (mtp) REVERT: A 3719 MET cc_start: 0.8324 (tpp) cc_final: 0.8042 (tpt) REVERT: A 4048 PHE cc_start: 0.8929 (t80) cc_final: 0.8726 (t80) REVERT: A 4060 GLN cc_start: 0.8578 (tp40) cc_final: 0.8345 (tp40) REVERT: A 4558 HIS cc_start: 0.7513 (m-70) cc_final: 0.7284 (m90) REVERT: A 4748 MET cc_start: 0.7293 (mpt) cc_final: 0.6978 (mpt) REVERT: G 61 GLU cc_start: 0.8047 (tp30) cc_final: 0.7659 (tt0) REVERT: B 895 MET cc_start: 0.9004 (ptt) cc_final: 0.8332 (ppp) REVERT: B 964 MET cc_start: -0.1698 (mpt) cc_final: -0.2115 (pmm) REVERT: B 1035 TYR cc_start: 0.7283 (t80) cc_final: 0.6881 (t80) REVERT: B 1051 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8065 (mtm180) REVERT: B 1165 MET cc_start: 0.8466 (mpp) cc_final: 0.8231 (mtm) REVERT: B 3121 LEU cc_start: 0.8850 (tt) cc_final: 0.8517 (tp) REVERT: B 3241 MET cc_start: 0.7782 (tmm) cc_final: 0.7442 (tmm) REVERT: B 3246 MET cc_start: 0.8934 (mtp) cc_final: 0.8577 (mtt) REVERT: B 3315 LEU cc_start: 0.9323 (mm) cc_final: 0.9114 (mm) REVERT: B 3719 MET cc_start: 0.8304 (tpp) cc_final: 0.8005 (tpt) REVERT: B 3854 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8325 (t80) REVERT: B 3888 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: B 4048 PHE cc_start: 0.8999 (t80) cc_final: 0.8767 (t80) REVERT: C 895 MET cc_start: 0.8889 (ptt) cc_final: 0.8187 (ppp) REVERT: C 934 GLN cc_start: 0.8520 (pp30) cc_final: 0.8212 (pp30) REVERT: C 964 MET cc_start: -0.2176 (mpt) cc_final: -0.2579 (pmm) REVERT: C 1031 ARG cc_start: 0.7745 (ttt-90) cc_final: 0.7140 (mmm160) REVERT: C 1035 TYR cc_start: 0.7261 (t80) cc_final: 0.6824 (t80) REVERT: C 1051 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7928 (mtt180) REVERT: C 2162 MET cc_start: 0.8909 (mmm) cc_final: 0.8695 (mmp) REVERT: C 3130 CYS cc_start: 0.8420 (m) cc_final: 0.7952 (m) REVERT: C 3214 LEU cc_start: 0.9283 (mp) cc_final: 0.8985 (mp) REVERT: C 3220 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8320 (mm-30) REVERT: C 3235 MET cc_start: 0.7555 (pmm) cc_final: 0.6725 (ppp) REVERT: C 3241 MET cc_start: 0.8009 (tmm) cc_final: 0.7560 (tmm) REVERT: C 3318 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6757 (t70) REVERT: C 3981 MET cc_start: 0.8700 (tmm) cc_final: 0.8409 (tmt) REVERT: C 4048 PHE cc_start: 0.8720 (t80) cc_final: 0.8359 (t80) REVERT: C 4246 PHE cc_start: 0.8142 (t80) cc_final: 0.7672 (t80) REVERT: C 4558 HIS cc_start: 0.7434 (m90) cc_final: 0.7136 (m-70) REVERT: C 4660 PHE cc_start: 0.8056 (p90) cc_final: 0.7783 (p90) REVERT: D 128 MET cc_start: 0.8756 (mtt) cc_final: 0.8502 (mtp) REVERT: D 895 MET cc_start: 0.8742 (ptt) cc_final: 0.8229 (ppp) REVERT: D 995 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7792 (mpp) REVERT: D 1035 TYR cc_start: 0.7470 (t80) cc_final: 0.6967 (t80) REVERT: D 1058 LEU cc_start: 0.8318 (mt) cc_final: 0.8064 (mt) REVERT: D 2793 ARG cc_start: 0.7492 (mmm160) cc_final: 0.6652 (mmm160) REVERT: D 2798 MET cc_start: 0.6236 (tpt) cc_final: 0.5433 (tpt) REVERT: D 3130 CYS cc_start: 0.8420 (m) cc_final: 0.7937 (m) REVERT: D 3219 VAL cc_start: 0.9152 (t) cc_final: 0.8675 (p) REVERT: D 3220 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8266 (mm-30) REVERT: D 3235 MET cc_start: 0.7555 (pmm) cc_final: 0.7015 (ppp) REVERT: D 3246 MET cc_start: 0.8939 (mtp) cc_final: 0.8618 (mtt) REVERT: D 3302 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7834 (t80) REVERT: D 3314 LEU cc_start: 0.9430 (mm) cc_final: 0.9209 (mp) REVERT: D 3689 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: D 3854 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8334 (t80) REVERT: D 3981 MET cc_start: 0.8668 (tmm) cc_final: 0.8418 (tmm) REVERT: D 4048 PHE cc_start: 0.8794 (t80) cc_final: 0.8556 (t80) outliers start: 140 outliers final: 43 residues processed: 1035 average time/residue: 2.0346 time to fit residues: 3054.9678 Evaluate side-chains 980 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 926 time to evaluate : 11.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 2444 THR Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3149 GLU Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2173 GLU Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2444 THR Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3166 PHE Chi-restraints excluded: chain B residue 3306 ILE Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2444 THR Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2688 MET Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3166 PHE Chi-restraints excluded: chain C residue 3318 HIS Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 995 MET Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3149 GLU Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3302 PHE Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 3854 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 20.0000 chunk 1504 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 980 optimal weight: 20.0000 chunk 412 optimal weight: 6.9990 chunk 1671 optimal weight: 8.9990 chunk 1387 optimal weight: 6.9990 chunk 774 optimal weight: 10.0000 chunk 139 optimal weight: 0.3980 chunk 553 optimal weight: 0.9990 chunk 877 optimal weight: 5.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN F 44 ASN G 44 ASN B 12 GLN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4088 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 141708 Z= 0.315 Angle : 0.619 17.516 191468 Z= 0.309 Chirality : 0.042 0.382 20988 Planarity : 0.004 0.073 24596 Dihedral : 6.071 117.428 19106 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 0.92 % Allowed : 9.50 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 1.06 (0.07), residues: 17212 helix: 1.89 (0.06), residues: 8908 sheet: -0.30 (0.13), residues: 1724 loop : -0.65 (0.08), residues: 6580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2741 HIS 0.011 0.001 HIS B4057 PHE 0.031 0.002 PHE A4016 TYR 0.054 0.001 TYR A 931 ARG 0.016 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 944 time to evaluate : 12.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 964 MET cc_start: -0.1599 (mpt) cc_final: -0.2110 (pmm) REVERT: A 981 MET cc_start: 0.7151 (ppp) cc_final: 0.6925 (ppp) REVERT: A 995 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7748 (mpp) REVERT: A 1035 TYR cc_start: 0.7540 (t80) cc_final: 0.7006 (t80) REVERT: A 1058 LEU cc_start: 0.8492 (mt) cc_final: 0.8282 (mp) REVERT: A 1215 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8283 (mtt) REVERT: A 2732 TRP cc_start: 0.7838 (t60) cc_final: 0.7607 (t60) REVERT: A 2793 ARG cc_start: 0.7402 (mmm160) cc_final: 0.6656 (mmm160) REVERT: A 2798 MET cc_start: 0.6135 (tpt) cc_final: 0.5393 (tpt) REVERT: A 2958 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7671 (tp40) REVERT: A 3220 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 3235 MET cc_start: 0.7638 (pmm) cc_final: 0.7187 (ppp) REVERT: A 3246 MET cc_start: 0.8856 (mtp) cc_final: 0.8573 (mtt) REVERT: A 3315 LEU cc_start: 0.9208 (mm) cc_final: 0.8928 (mm) REVERT: A 3319 PHE cc_start: 0.8129 (m-80) cc_final: 0.7827 (m-80) REVERT: A 3719 MET cc_start: 0.8318 (tpp) cc_final: 0.8020 (tpt) REVERT: A 3854 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8253 (t80) REVERT: A 4048 PHE cc_start: 0.8907 (t80) cc_final: 0.8451 (t80) REVERT: A 4060 GLN cc_start: 0.8599 (tp40) cc_final: 0.8361 (tp40) REVERT: A 4558 HIS cc_start: 0.7486 (m-70) cc_final: 0.7249 (m90) REVERT: A 4748 MET cc_start: 0.7305 (mpt) cc_final: 0.6989 (mpt) REVERT: G 61 GLU cc_start: 0.8066 (tp30) cc_final: 0.7685 (tt0) REVERT: B 892 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8399 (pt) REVERT: B 895 MET cc_start: 0.9028 (ptt) cc_final: 0.8585 (ppp) REVERT: B 934 GLN cc_start: 0.8883 (pt0) cc_final: 0.8657 (mm-40) REVERT: B 964 MET cc_start: -0.1665 (mpt) cc_final: -0.2103 (pmm) REVERT: B 1035 TYR cc_start: 0.7311 (t80) cc_final: 0.6909 (t80) REVERT: B 1165 MET cc_start: 0.8466 (mpp) cc_final: 0.8194 (mtm) REVERT: B 1215 MET cc_start: 0.8628 (mmm) cc_final: 0.8299 (mtt) REVERT: B 2512 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7229 (tpp) REVERT: B 3121 LEU cc_start: 0.8865 (tt) cc_final: 0.8520 (tp) REVERT: B 3235 MET cc_start: 0.7540 (pmm) cc_final: 0.6989 (pmm) REVERT: B 3241 MET cc_start: 0.7801 (tmm) cc_final: 0.7407 (tmm) REVERT: B 3246 MET cc_start: 0.8931 (mtp) cc_final: 0.8581 (mtt) REVERT: B 3719 MET cc_start: 0.8291 (tpp) cc_final: 0.8001 (tpt) REVERT: B 3854 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8332 (t80) REVERT: B 3888 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: B 4048 PHE cc_start: 0.9005 (t80) cc_final: 0.8802 (t80) REVERT: C 895 MET cc_start: 0.8924 (ptt) cc_final: 0.8495 (ppp) REVERT: C 934 GLN cc_start: 0.8530 (pp30) cc_final: 0.8212 (pp30) REVERT: C 964 MET cc_start: -0.2212 (mpt) cc_final: -0.2523 (pmm) REVERT: C 1031 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7218 (mmm160) REVERT: C 1035 TYR cc_start: 0.7336 (t80) cc_final: 0.6900 (t80) REVERT: C 1215 MET cc_start: 0.8661 (mmm) cc_final: 0.8413 (mtt) REVERT: C 1477 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7637 (m-70) REVERT: C 3130 CYS cc_start: 0.8440 (m) cc_final: 0.7993 (m) REVERT: C 3214 LEU cc_start: 0.9288 (mp) cc_final: 0.8974 (mp) REVERT: C 3220 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8360 (mm-30) REVERT: C 3235 MET cc_start: 0.7657 (pmm) cc_final: 0.6949 (ppp) REVERT: C 3241 MET cc_start: 0.7922 (tmm) cc_final: 0.7438 (tmm) REVERT: C 3255 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: C 3281 LEU cc_start: 0.8716 (mp) cc_final: 0.8471 (pt) REVERT: C 3302 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 3854 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8320 (t80) REVERT: C 3981 MET cc_start: 0.8690 (tmm) cc_final: 0.8391 (tmt) REVERT: C 4048 PHE cc_start: 0.8716 (t80) cc_final: 0.8386 (t80) REVERT: C 4246 PHE cc_start: 0.8180 (t80) cc_final: 0.7651 (t80) REVERT: C 4558 HIS cc_start: 0.7434 (m90) cc_final: 0.7118 (m-70) REVERT: C 4660 PHE cc_start: 0.8047 (p90) cc_final: 0.7824 (p90) REVERT: D 128 MET cc_start: 0.8764 (mtt) cc_final: 0.8506 (mtp) REVERT: D 895 MET cc_start: 0.8776 (ptt) cc_final: 0.8231 (ppp) REVERT: D 1035 TYR cc_start: 0.7472 (t80) cc_final: 0.6990 (t80) REVERT: D 2798 MET cc_start: 0.6217 (tpt) cc_final: 0.5380 (tpt) REVERT: D 3130 CYS cc_start: 0.8462 (m) cc_final: 0.7991 (m) REVERT: D 3220 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8311 (mm-30) REVERT: D 3235 MET cc_start: 0.7620 (pmm) cc_final: 0.7180 (ppp) REVERT: D 3246 MET cc_start: 0.8926 (mtp) cc_final: 0.8621 (mtt) REVERT: D 3302 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7830 (t80) REVERT: D 3854 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8347 (t80) REVERT: D 3981 MET cc_start: 0.8670 (tmm) cc_final: 0.8442 (tmm) REVERT: D 4048 PHE cc_start: 0.8805 (t80) cc_final: 0.8581 (t80) outliers start: 132 outliers final: 45 residues processed: 1021 average time/residue: 2.0779 time to fit residues: 3079.4205 Evaluate side-chains 974 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 916 time to evaluate : 13.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 2444 THR Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2444 THR Chi-restraints excluded: chain B residue 2512 MET Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3166 PHE Chi-restraints excluded: chain B residue 3306 ILE Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1477 HIS Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2444 THR Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2688 MET Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3255 GLU Chi-restraints excluded: chain C residue 3302 PHE Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1933 VAL Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2444 THR Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2770 ILE Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3302 PHE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 0.4980 chunk 188 optimal weight: 0.8980 chunk 952 optimal weight: 10.0000 chunk 1220 optimal weight: 7.9990 chunk 945 optimal weight: 4.9990 chunk 1407 optimal weight: 10.0000 chunk 933 optimal weight: 3.9990 chunk 1665 optimal weight: 9.9990 chunk 1042 optimal weight: 8.9990 chunk 1015 optimal weight: 6.9990 chunk 768 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN F 44 ASN G 44 ASN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3279 ASN ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3308 ASN ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 141708 Z= 0.301 Angle : 0.622 18.546 191468 Z= 0.310 Chirality : 0.042 0.599 20988 Planarity : 0.004 0.076 24596 Dihedral : 5.984 116.350 19106 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 0.84 % Allowed : 9.98 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 1.07 (0.07), residues: 17212 helix: 1.90 (0.06), residues: 8912 sheet: -0.31 (0.13), residues: 1724 loop : -0.65 (0.08), residues: 6576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B3250 HIS 0.011 0.001 HIS C4057 PHE 0.031 0.001 PHE A4016 TYR 0.052 0.001 TYR A 931 ARG 0.017 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 936 time to evaluate : 11.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 892 LEU cc_start: 0.8700 (mp) cc_final: 0.8498 (pt) REVERT: A 895 MET cc_start: 0.8822 (ptt) cc_final: 0.8354 (ppp) REVERT: A 964 MET cc_start: -0.1570 (mpt) cc_final: -0.2077 (pmm) REVERT: A 995 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7691 (mpp) REVERT: A 1035 TYR cc_start: 0.7542 (t80) cc_final: 0.7034 (t80) REVERT: A 1215 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: A 2732 TRP cc_start: 0.7833 (t60) cc_final: 0.7615 (t60) REVERT: A 2734 MET cc_start: 0.6650 (mpt) cc_final: 0.6445 (mpt) REVERT: A 2798 MET cc_start: 0.6156 (tpt) cc_final: 0.5405 (tpt) REVERT: A 2958 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7712 (tp40) REVERT: A 3220 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8219 (mm-30) REVERT: A 3235 MET cc_start: 0.7649 (pmm) cc_final: 0.6967 (ppp) REVERT: A 3246 MET cc_start: 0.8843 (mtp) cc_final: 0.8563 (mtt) REVERT: A 3315 LEU cc_start: 0.9218 (mm) cc_final: 0.8909 (mm) REVERT: A 3319 PHE cc_start: 0.8215 (m-80) cc_final: 0.7941 (m-80) REVERT: A 3323 MET cc_start: 0.8652 (mpp) cc_final: 0.8337 (pmm) REVERT: A 3719 MET cc_start: 0.8298 (tpp) cc_final: 0.8012 (tpt) REVERT: A 3854 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8248 (t80) REVERT: A 4048 PHE cc_start: 0.8864 (t80) cc_final: 0.8443 (t80) REVERT: A 4060 GLN cc_start: 0.8601 (tp40) cc_final: 0.8363 (tp40) REVERT: A 4558 HIS cc_start: 0.7492 (m-70) cc_final: 0.7262 (m90) REVERT: G 61 GLU cc_start: 0.8069 (tp30) cc_final: 0.7693 (tt0) REVERT: B 892 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8418 (pt) REVERT: B 895 MET cc_start: 0.9031 (ptt) cc_final: 0.8572 (ppp) REVERT: B 934 GLN cc_start: 0.8864 (pt0) cc_final: 0.8627 (mm-40) REVERT: B 964 MET cc_start: -0.1708 (mpt) cc_final: -0.2133 (pmm) REVERT: B 1035 TYR cc_start: 0.7343 (t80) cc_final: 0.6954 (t80) REVERT: B 1165 MET cc_start: 0.8472 (mpp) cc_final: 0.8179 (mtm) REVERT: B 1215 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8408 (mtt) REVERT: B 2175 MET cc_start: 0.8246 (ttp) cc_final: 0.8004 (ttm) REVERT: B 2689 MET cc_start: 0.5862 (ppp) cc_final: 0.5493 (pmm) REVERT: B 3121 LEU cc_start: 0.8861 (tt) cc_final: 0.8513 (tp) REVERT: B 3241 MET cc_start: 0.7798 (tmm) cc_final: 0.7304 (tmm) REVERT: B 3246 MET cc_start: 0.8944 (mtp) cc_final: 0.8584 (mtt) REVERT: B 3719 MET cc_start: 0.8298 (tpp) cc_final: 0.8002 (tpt) REVERT: B 3854 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8329 (t80) REVERT: B 3888 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: B 4048 PHE cc_start: 0.8999 (t80) cc_final: 0.8601 (t80) REVERT: C 895 MET cc_start: 0.8938 (ptt) cc_final: 0.8467 (ppp) REVERT: C 934 GLN cc_start: 0.8529 (pp30) cc_final: 0.8212 (pp30) REVERT: C 964 MET cc_start: -0.2176 (mpt) cc_final: -0.2503 (pmm) REVERT: C 1031 ARG cc_start: 0.7728 (ttt-90) cc_final: 0.7170 (mmm160) REVERT: C 1035 TYR cc_start: 0.7296 (t80) cc_final: 0.6860 (t80) REVERT: C 1215 MET cc_start: 0.8646 (mmm) cc_final: 0.8353 (mtt) REVERT: C 1477 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7639 (m-70) REVERT: C 3130 CYS cc_start: 0.8420 (m) cc_final: 0.7972 (m) REVERT: C 3214 LEU cc_start: 0.9297 (mp) cc_final: 0.8999 (mp) REVERT: C 3220 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8359 (mm-30) REVERT: C 3235 MET cc_start: 0.7681 (pmm) cc_final: 0.7011 (ppp) REVERT: C 3241 MET cc_start: 0.7995 (tmm) cc_final: 0.7455 (tmm) REVERT: C 3246 MET cc_start: 0.8967 (mtp) cc_final: 0.8532 (mtt) REVERT: C 3255 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: C 3279 ASN cc_start: 0.8595 (m110) cc_final: 0.8258 (p0) REVERT: C 3689 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7478 (mpp) REVERT: C 3854 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8320 (t80) REVERT: C 3981 MET cc_start: 0.8694 (tmm) cc_final: 0.8390 (tmt) REVERT: C 4048 PHE cc_start: 0.8729 (t80) cc_final: 0.8349 (t80) REVERT: C 4246 PHE cc_start: 0.8181 (t80) cc_final: 0.7659 (t80) REVERT: C 4558 HIS cc_start: 0.7435 (m90) cc_final: 0.7099 (m-70) REVERT: C 4660 PHE cc_start: 0.8035 (p90) cc_final: 0.7827 (p90) REVERT: D 128 MET cc_start: 0.8759 (mtt) cc_final: 0.8503 (mtp) REVERT: D 277 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8654 (tt) REVERT: D 895 MET cc_start: 0.8850 (ptt) cc_final: 0.8317 (ppp) REVERT: D 995 MET cc_start: 0.8020 (mpp) cc_final: 0.7760 (mpp) REVERT: D 1035 TYR cc_start: 0.7518 (t80) cc_final: 0.7021 (t80) REVERT: D 2732 TRP cc_start: 0.7712 (t60) cc_final: 0.7463 (t60) REVERT: D 3130 CYS cc_start: 0.8473 (m) cc_final: 0.8024 (m) REVERT: D 3219 VAL cc_start: 0.9201 (t) cc_final: 0.8636 (p) REVERT: D 3220 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8309 (mm-30) REVERT: D 3235 MET cc_start: 0.7657 (pmm) cc_final: 0.6926 (ppp) REVERT: D 3246 MET cc_start: 0.8918 (mtp) cc_final: 0.8633 (mtt) REVERT: D 3314 LEU cc_start: 0.9425 (mm) cc_final: 0.9200 (mm) REVERT: D 3323 MET cc_start: 0.8433 (mpp) cc_final: 0.8199 (pmm) REVERT: D 3854 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8350 (t80) REVERT: D 3981 MET cc_start: 0.8683 (tmm) cc_final: 0.8411 (tmm) REVERT: D 4048 PHE cc_start: 0.8757 (t80) cc_final: 0.8490 (t80) outliers start: 120 outliers final: 51 residues processed: 1010 average time/residue: 2.0456 time to fit residues: 2998.9950 Evaluate side-chains 984 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 920 time to evaluate : 11.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 2444 THR Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1215 MET Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2444 THR Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3166 PHE Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1477 HIS Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 1933 VAL Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2444 THR Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2688 MET Chi-restraints excluded: chain C residue 3029 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3255 GLU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 887 GLU Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1933 VAL Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2444 THR Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2770 ILE Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 9.9990 chunk 665 optimal weight: 3.9990 chunk 994 optimal weight: 7.9990 chunk 501 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 1058 optimal weight: 3.9990 chunk 1134 optimal weight: 9.9990 chunk 823 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 1309 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3955 GLN A3975 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4178 ASN E 44 ASN F 44 ASN G 44 ASN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B2802 ASN ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS C3955 GLN C3975 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 HIS ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 141708 Z= 0.391 Angle : 0.662 19.787 191468 Z= 0.328 Chirality : 0.044 0.595 20988 Planarity : 0.005 0.082 24596 Dihedral : 5.995 115.724 19106 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 0.86 % Allowed : 10.18 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.06), residues: 17212 helix: 1.83 (0.06), residues: 8904 sheet: -0.34 (0.13), residues: 1716 loop : -0.67 (0.08), residues: 6592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C3250 HIS 0.010 0.001 HIS C3700 PHE 0.032 0.002 PHE A4016 TYR 0.046 0.002 TYR A 931 ARG 0.020 0.001 ARG D2793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 940 time to evaluate : 11.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 895 MET cc_start: 0.8847 (ptt) cc_final: 0.8387 (ppp) REVERT: A 964 MET cc_start: -0.1519 (mpt) cc_final: -0.2031 (pmm) REVERT: A 995 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7633 (mpp) REVERT: A 1035 TYR cc_start: 0.7612 (t80) cc_final: 0.7083 (t80) REVERT: A 1050 LEU cc_start: 0.9193 (pt) cc_final: 0.8751 (tp) REVERT: A 1051 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7898 (mtm180) REVERT: A 1215 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8391 (mtt) REVERT: A 2689 MET cc_start: 0.5549 (tpp) cc_final: 0.5037 (tpt) REVERT: A 2732 TRP cc_start: 0.7806 (t60) cc_final: 0.7568 (t60) REVERT: A 2793 ARG cc_start: 0.7283 (mmm160) cc_final: 0.6076 (mmm160) REVERT: A 2958 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7733 (tp40) REVERT: A 3220 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 3235 MET cc_start: 0.7658 (pmm) cc_final: 0.7047 (ppp) REVERT: A 3246 MET cc_start: 0.8885 (mtp) cc_final: 0.8638 (mtt) REVERT: A 3315 LEU cc_start: 0.9260 (mm) cc_final: 0.8980 (mm) REVERT: A 3319 PHE cc_start: 0.8268 (m-80) cc_final: 0.7939 (m-80) REVERT: A 3689 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7591 (mpp) REVERT: A 3719 MET cc_start: 0.8304 (tpp) cc_final: 0.8046 (tpt) REVERT: A 3854 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8269 (t80) REVERT: A 4048 PHE cc_start: 0.8849 (t80) cc_final: 0.8481 (t80) REVERT: A 4060 GLN cc_start: 0.8603 (tp40) cc_final: 0.8365 (tp40) REVERT: A 4558 HIS cc_start: 0.7537 (m-70) cc_final: 0.7326 (m90) REVERT: G 30 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7207 (mtp) REVERT: G 61 GLU cc_start: 0.8066 (tp30) cc_final: 0.7713 (tt0) REVERT: B 934 GLN cc_start: 0.8869 (pt0) cc_final: 0.8639 (mm-40) REVERT: B 964 MET cc_start: -0.1903 (mpt) cc_final: -0.2294 (pmm) REVERT: B 1035 TYR cc_start: 0.7430 (t80) cc_final: 0.7009 (t80) REVERT: B 1165 MET cc_start: 0.8481 (mpp) cc_final: 0.8272 (mtm) REVERT: B 2175 MET cc_start: 0.8261 (ttp) cc_final: 0.8053 (ttm) REVERT: B 3121 LEU cc_start: 0.8862 (tt) cc_final: 0.8518 (tp) REVERT: B 3235 MET cc_start: 0.7652 (pmm) cc_final: 0.7098 (pmm) REVERT: B 3241 MET cc_start: 0.7823 (tmm) cc_final: 0.7438 (tmm) REVERT: B 3246 MET cc_start: 0.8952 (mtp) cc_final: 0.8597 (mtt) REVERT: B 3250 TRP cc_start: 0.8288 (t60) cc_final: 0.8070 (t60) REVERT: B 3279 ASN cc_start: 0.8458 (m110) cc_final: 0.7964 (t0) REVERT: B 3302 PHE cc_start: 0.8015 (m-80) cc_final: 0.7457 (t80) REVERT: B 3689 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7575 (mpp) REVERT: B 3719 MET cc_start: 0.8294 (tpp) cc_final: 0.8056 (tpt) REVERT: B 3854 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 3888 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: B 4048 PHE cc_start: 0.8988 (t80) cc_final: 0.8787 (t80) REVERT: C 895 MET cc_start: 0.8941 (ptt) cc_final: 0.8474 (ppp) REVERT: C 934 GLN cc_start: 0.8528 (pp30) cc_final: 0.8231 (pp30) REVERT: C 964 MET cc_start: -0.2253 (mpt) cc_final: -0.2575 (pmm) REVERT: C 1031 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7294 (mmm160) REVERT: C 1035 TYR cc_start: 0.7426 (t80) cc_final: 0.6964 (t80) REVERT: C 1215 MET cc_start: 0.8645 (mmm) cc_final: 0.8414 (mtt) REVERT: C 1477 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7650 (m-70) REVERT: C 3130 CYS cc_start: 0.8444 (m) cc_final: 0.8000 (m) REVERT: C 3214 LEU cc_start: 0.9314 (mp) cc_final: 0.8984 (mp) REVERT: C 3220 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8427 (mm-30) REVERT: C 3235 MET cc_start: 0.7708 (pmm) cc_final: 0.7019 (ppp) REVERT: C 3241 MET cc_start: 0.7998 (tmm) cc_final: 0.7461 (tmm) REVERT: C 3246 MET cc_start: 0.8995 (mtp) cc_final: 0.8554 (mtt) REVERT: C 3250 TRP cc_start: 0.8502 (t60) cc_final: 0.8046 (t60) REVERT: C 3255 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: C 3279 ASN cc_start: 0.8646 (m110) cc_final: 0.8330 (p0) REVERT: C 3689 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7555 (mpp) REVERT: C 3854 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8347 (t80) REVERT: C 3981 MET cc_start: 0.8678 (tmm) cc_final: 0.8351 (tmt) REVERT: C 4048 PHE cc_start: 0.8725 (t80) cc_final: 0.8410 (t80) REVERT: C 4246 PHE cc_start: 0.8151 (t80) cc_final: 0.7659 (t80) REVERT: C 4558 HIS cc_start: 0.7456 (m90) cc_final: 0.7125 (m-70) REVERT: D 128 MET cc_start: 0.8777 (mtt) cc_final: 0.8520 (mtp) REVERT: D 895 MET cc_start: 0.8868 (ptt) cc_final: 0.8344 (ppp) REVERT: D 995 MET cc_start: 0.8021 (mpp) cc_final: 0.7712 (mpp) REVERT: D 1035 TYR cc_start: 0.7575 (t80) cc_final: 0.7036 (t80) REVERT: D 2732 TRP cc_start: 0.7755 (t60) cc_final: 0.7497 (t60) REVERT: D 2768 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7998 (tptt) REVERT: D 2793 ARG cc_start: 0.7437 (mmm160) cc_final: 0.6697 (mmm160) REVERT: D 3130 CYS cc_start: 0.8477 (m) cc_final: 0.8024 (m) REVERT: D 3220 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8386 (mm-30) REVERT: D 3235 MET cc_start: 0.7686 (pmm) cc_final: 0.6958 (ppp) REVERT: D 3246 MET cc_start: 0.8971 (mtp) cc_final: 0.8689 (mtt) REVERT: D 3854 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8379 (t80) REVERT: D 4048 PHE cc_start: 0.8768 (t80) cc_final: 0.8565 (t80) outliers start: 123 outliers final: 54 residues processed: 1007 average time/residue: 2.0547 time to fit residues: 3000.6566 Evaluate side-chains 992 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 925 time to evaluate : 11.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 2444 THR Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 1933 VAL Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2444 THR Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3166 PHE Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4120 GLU Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 933 LEU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1477 HIS Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 1933 VAL Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2444 THR Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2688 MET Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3166 PHE Chi-restraints excluded: chain C residue 3255 GLU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 4120 GLU Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1933 VAL Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2444 THR Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2770 ILE Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 9.9990 chunk 1595 optimal weight: 4.9990 chunk 1455 optimal weight: 0.9990 chunk 1552 optimal weight: 20.0000 chunk 934 optimal weight: 6.9990 chunk 676 optimal weight: 20.0000 chunk 1218 optimal weight: 10.0000 chunk 476 optimal weight: 4.9990 chunk 1402 optimal weight: 20.0000 chunk 1467 optimal weight: 7.9990 chunk 1546 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3279 ASN A3955 GLN A3975 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN F 44 ASN G 44 ASN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3257 ASN ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3882 GLN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS C3955 GLN C3975 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 HIS D2802 ASN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 141708 Z= 0.418 Angle : 0.677 20.568 191468 Z= 0.336 Chirality : 0.044 0.617 20988 Planarity : 0.005 0.089 24596 Dihedral : 6.021 114.684 19106 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 0.70 % Allowed : 10.48 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.06), residues: 17212 helix: 1.78 (0.06), residues: 8900 sheet: -0.37 (0.13), residues: 1716 loop : -0.70 (0.08), residues: 6596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A2741 HIS 0.010 0.001 HIS C3700 PHE 0.031 0.002 PHE A4016 TYR 0.053 0.002 TYR A 931 ARG 0.019 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 936 time to evaluate : 11.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 892 LEU cc_start: 0.8906 (pt) cc_final: 0.8569 (pt) REVERT: A 895 MET cc_start: 0.8809 (ptt) cc_final: 0.8369 (ppp) REVERT: A 964 MET cc_start: -0.1581 (mpt) cc_final: -0.2115 (pmm) REVERT: A 1035 TYR cc_start: 0.7654 (t80) cc_final: 0.7120 (t80) REVERT: A 1064 LEU cc_start: 0.8682 (mm) cc_final: 0.8442 (mm) REVERT: A 2162 MET cc_start: 0.8876 (mmm) cc_final: 0.8674 (mmp) REVERT: A 2689 MET cc_start: 0.5452 (tpp) cc_final: 0.4902 (tpt) REVERT: A 2732 TRP cc_start: 0.7836 (t60) cc_final: 0.7597 (t60) REVERT: A 2958 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7800 (tp40) REVERT: A 3220 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 3235 MET cc_start: 0.7710 (pmm) cc_final: 0.7103 (ppp) REVERT: A 3246 MET cc_start: 0.8914 (mtp) cc_final: 0.8645 (mtt) REVERT: A 3315 LEU cc_start: 0.9264 (mm) cc_final: 0.9037 (mm) REVERT: A 3689 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7540 (mpp) REVERT: A 3719 MET cc_start: 0.8327 (tpp) cc_final: 0.8070 (tpt) REVERT: A 3854 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8272 (t80) REVERT: A 4048 PHE cc_start: 0.8810 (t80) cc_final: 0.8489 (t80) REVERT: A 4660 PHE cc_start: 0.8384 (p90) cc_final: 0.8182 (p90) REVERT: F 30 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7293 (mpp) REVERT: G 30 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7209 (mtp) REVERT: B 892 LEU cc_start: 0.8623 (pt) cc_final: 0.8218 (pt) REVERT: B 895 MET cc_start: 0.8742 (ptt) cc_final: 0.8448 (ppp) REVERT: B 964 MET cc_start: -0.1696 (mpt) cc_final: -0.2104 (pmm) REVERT: B 1035 TYR cc_start: 0.7440 (t80) cc_final: 0.7009 (t80) REVERT: B 1165 MET cc_start: 0.8475 (mpp) cc_final: 0.8171 (mtm) REVERT: B 2175 MET cc_start: 0.8254 (ttp) cc_final: 0.8046 (ttm) REVERT: B 2512 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7230 (tpp) REVERT: B 2689 MET cc_start: 0.5840 (ppp) cc_final: 0.5233 (pmm) REVERT: B 3235 MET cc_start: 0.7706 (pmm) cc_final: 0.7185 (pmm) REVERT: B 3241 MET cc_start: 0.7874 (tmm) cc_final: 0.7484 (tmm) REVERT: B 3246 MET cc_start: 0.8954 (mtp) cc_final: 0.8601 (mtt) REVERT: B 3279 ASN cc_start: 0.8494 (m110) cc_final: 0.7885 (t0) REVERT: B 3719 MET cc_start: 0.8305 (tpp) cc_final: 0.8038 (tpt) REVERT: B 3854 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8363 (t80) REVERT: B 3888 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: B 4048 PHE cc_start: 0.8969 (t80) cc_final: 0.8742 (t80) REVERT: C 317 MET cc_start: 0.7719 (ttp) cc_final: 0.7452 (ttm) REVERT: C 895 MET cc_start: 0.8946 (ptt) cc_final: 0.8456 (ppp) REVERT: C 964 MET cc_start: -0.2306 (mpt) cc_final: -0.2654 (pmm) REVERT: C 999 LEU cc_start: 0.8939 (mt) cc_final: 0.8724 (mt) REVERT: C 1031 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7540 (mmm160) REVERT: C 1035 TYR cc_start: 0.7476 (t80) cc_final: 0.7005 (t80) REVERT: C 1215 MET cc_start: 0.8650 (mmm) cc_final: 0.8262 (mtt) REVERT: C 1477 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7653 (m-70) REVERT: C 2134 MET cc_start: 0.9026 (tpt) cc_final: 0.8811 (tpt) REVERT: C 3130 CYS cc_start: 0.8450 (m) cc_final: 0.8017 (m) REVERT: C 3214 LEU cc_start: 0.9323 (mp) cc_final: 0.9001 (mp) REVERT: C 3220 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8453 (mm-30) REVERT: C 3235 MET cc_start: 0.7728 (pmm) cc_final: 0.7017 (ppp) REVERT: C 3241 MET cc_start: 0.8001 (tmm) cc_final: 0.7534 (tmm) REVERT: C 3246 MET cc_start: 0.9013 (mtp) cc_final: 0.8574 (mtt) REVERT: C 3250 TRP cc_start: 0.8513 (t60) cc_final: 0.8072 (t60) REVERT: C 3255 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: C 3279 ASN cc_start: 0.8706 (m110) cc_final: 0.8386 (p0) REVERT: C 3689 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7564 (mpp) REVERT: C 3854 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8349 (t80) REVERT: C 3981 MET cc_start: 0.8672 (tmm) cc_final: 0.8415 (tmt) REVERT: C 4048 PHE cc_start: 0.8723 (t80) cc_final: 0.8408 (t80) REVERT: C 4246 PHE cc_start: 0.8133 (t80) cc_final: 0.7656 (t80) REVERT: C 4558 HIS cc_start: 0.7481 (m90) cc_final: 0.7146 (m-70) REVERT: D 128 MET cc_start: 0.8783 (mtt) cc_final: 0.8526 (mtp) REVERT: D 317 MET cc_start: 0.7699 (ttp) cc_final: 0.7406 (ttm) REVERT: D 895 MET cc_start: 0.8822 (ptt) cc_final: 0.8325 (ppp) REVERT: D 1035 TYR cc_start: 0.7632 (t80) cc_final: 0.7071 (t80) REVERT: D 1051 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7876 (ptp-170) REVERT: D 1477 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7631 (m-70) REVERT: D 2732 TRP cc_start: 0.7750 (t60) cc_final: 0.7497 (t60) REVERT: D 3130 CYS cc_start: 0.8475 (m) cc_final: 0.8011 (m) REVERT: D 3220 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8426 (mm-30) REVERT: D 3235 MET cc_start: 0.7726 (pmm) cc_final: 0.6987 (ppp) REVERT: D 3854 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8391 (t80) REVERT: D 4048 PHE cc_start: 0.8754 (t80) cc_final: 0.8483 (t80) outliers start: 98 outliers final: 50 residues processed: 992 average time/residue: 2.0272 time to fit residues: 2912.1818 Evaluate side-chains 986 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 923 time to evaluate : 11.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1835 HIS Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 2444 THR Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3166 PHE Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 1835 HIS Chi-restraints excluded: chain B residue 1933 VAL Chi-restraints excluded: chain B residue 2279 MET Chi-restraints excluded: chain B residue 2444 THR Chi-restraints excluded: chain B residue 2512 MET Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3166 PHE Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1477 HIS Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 1933 VAL Chi-restraints excluded: chain C residue 2173 GLU Chi-restraints excluded: chain C residue 2279 MET Chi-restraints excluded: chain C residue 2444 THR Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2688 MET Chi-restraints excluded: chain C residue 2770 ILE Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3166 PHE Chi-restraints excluded: chain C residue 3255 GLU Chi-restraints excluded: chain C residue 3680 CYS Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1477 HIS Chi-restraints excluded: chain D residue 1896 MET Chi-restraints excluded: chain D residue 1933 VAL Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2444 THR Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 2770 ILE Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4019 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 3.9990 chunk 1641 optimal weight: 3.9990 chunk 1001 optimal weight: 9.9990 chunk 778 optimal weight: 0.7980 chunk 1140 optimal weight: 10.0000 chunk 1721 optimal weight: 0.9980 chunk 1584 optimal weight: 3.9990 chunk 1370 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 1058 optimal weight: 1.9990 chunk 840 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2802 ASN ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3308 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN F 44 ASN G 44 ASN B 12 GLN B 202 HIS ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2802 ASN ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3256 ASN ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2802 ASN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4055 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 141708 Z= 0.172 Angle : 0.630 21.707 191468 Z= 0.307 Chirality : 0.041 0.676 20988 Planarity : 0.004 0.084 24596 Dihedral : 5.828 113.423 19106 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 0.46 % Allowed : 10.89 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 1.16 (0.07), residues: 17212 helix: 1.95 (0.06), residues: 8912 sheet: -0.14 (0.13), residues: 1636 loop : -0.60 (0.08), residues: 6664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D2741 HIS 0.010 0.001 HIS C3700 PHE 0.027 0.001 PHE A4016 TYR 0.055 0.001 TYR C2801 ARG 0.020 0.000 ARG E 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 937 time to evaluate : 11.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 892 LEU cc_start: 0.8923 (pt) cc_final: 0.8606 (pt) REVERT: A 895 MET cc_start: 0.8783 (ptt) cc_final: 0.8387 (ppp) REVERT: A 964 MET cc_start: -0.1615 (mpt) cc_final: -0.2110 (pmm) REVERT: A 1035 TYR cc_start: 0.7504 (t80) cc_final: 0.7001 (t80) REVERT: A 1064 LEU cc_start: 0.8574 (mm) cc_final: 0.8295 (mm) REVERT: A 2175 MET cc_start: 0.8125 (ttp) cc_final: 0.7920 (ttm) REVERT: A 2689 MET cc_start: 0.5453 (tpp) cc_final: 0.5018 (tpt) REVERT: A 2793 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6424 (mmm160) REVERT: A 2798 MET cc_start: 0.5863 (tmt) cc_final: 0.5647 (tmt) REVERT: A 3220 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 3235 MET cc_start: 0.7669 (pmm) cc_final: 0.6901 (ppp) REVERT: A 3246 MET cc_start: 0.8795 (mtp) cc_final: 0.8566 (mtt) REVERT: A 3279 ASN cc_start: 0.8505 (m110) cc_final: 0.8244 (p0) REVERT: A 3689 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7470 (mpp) REVERT: A 3719 MET cc_start: 0.8253 (tpp) cc_final: 0.7990 (tpt) REVERT: A 3854 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 3954 MET cc_start: 0.8289 (mmm) cc_final: 0.7639 (mtm) REVERT: A 4048 PHE cc_start: 0.8763 (t80) cc_final: 0.8521 (t80) REVERT: A 4748 MET cc_start: 0.7327 (mpt) cc_final: 0.7042 (mpt) REVERT: A 4943 MET cc_start: 0.8687 (mtp) cc_final: 0.8464 (mtp) REVERT: G 30 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7204 (mtp) REVERT: B 892 LEU cc_start: 0.8669 (pt) cc_final: 0.8305 (pt) REVERT: B 895 MET cc_start: 0.8697 (ptt) cc_final: 0.8396 (ppp) REVERT: B 934 GLN cc_start: 0.8823 (pt0) cc_final: 0.8577 (mm-40) REVERT: B 964 MET cc_start: -0.1810 (mpt) cc_final: -0.2184 (pmm) REVERT: B 1035 TYR cc_start: 0.7318 (t80) cc_final: 0.6926 (t80) REVERT: B 1165 MET cc_start: 0.8483 (mpp) cc_final: 0.8260 (mtm) REVERT: B 1215 MET cc_start: 0.8636 (mmm) cc_final: 0.8432 (mtp) REVERT: B 1906 MET cc_start: 0.8221 (mmm) cc_final: 0.7981 (mmm) REVERT: B 2175 MET cc_start: 0.8102 (ttp) cc_final: 0.7778 (ttm) REVERT: B 2689 MET cc_start: 0.5877 (ppp) cc_final: 0.5238 (pmm) REVERT: B 3121 LEU cc_start: 0.8794 (tt) cc_final: 0.8514 (tp) REVERT: B 3235 MET cc_start: 0.7646 (pmm) cc_final: 0.7061 (pmm) REVERT: B 3241 MET cc_start: 0.7819 (tmm) cc_final: 0.7315 (tmm) REVERT: B 3246 MET cc_start: 0.8893 (mtp) cc_final: 0.8542 (mtt) REVERT: B 3719 MET cc_start: 0.8241 (tpp) cc_final: 0.7985 (tpt) REVERT: B 3888 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: C 895 MET cc_start: 0.8915 (ptt) cc_final: 0.8414 (ppp) REVERT: C 964 MET cc_start: -0.2288 (mpt) cc_final: -0.2608 (pmm) REVERT: C 1035 TYR cc_start: 0.7307 (t80) cc_final: 0.6867 (t80) REVERT: C 1215 MET cc_start: 0.8598 (mmm) cc_final: 0.8368 (mtt) REVERT: C 1477 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7617 (m-70) REVERT: C 3130 CYS cc_start: 0.8406 (m) cc_final: 0.7982 (m) REVERT: C 3214 LEU cc_start: 0.9307 (mp) cc_final: 0.8987 (mp) REVERT: C 3220 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8379 (mm-30) REVERT: C 3235 MET cc_start: 0.7734 (pmm) cc_final: 0.7041 (ppp) REVERT: C 3241 MET cc_start: 0.7950 (tmm) cc_final: 0.7401 (tmm) REVERT: C 3246 MET cc_start: 0.8940 (mtp) cc_final: 0.8474 (mtt) REVERT: C 3250 TRP cc_start: 0.8385 (t60) cc_final: 0.8073 (t60) REVERT: C 3255 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: C 3279 ASN cc_start: 0.8604 (m110) cc_final: 0.8357 (p0) REVERT: C 3981 MET cc_start: 0.8723 (tmm) cc_final: 0.8439 (tmt) REVERT: C 4048 PHE cc_start: 0.8675 (t80) cc_final: 0.8293 (t80) REVERT: C 4246 PHE cc_start: 0.8111 (t80) cc_final: 0.7612 (t80) REVERT: C 4558 HIS cc_start: 0.7456 (m90) cc_final: 0.7116 (m-70) REVERT: C 4943 MET cc_start: 0.8695 (mtp) cc_final: 0.8492 (mtp) REVERT: D 128 MET cc_start: 0.8726 (mtt) cc_final: 0.8473 (mtp) REVERT: D 317 MET cc_start: 0.7703 (ttp) cc_final: 0.7340 (ttt) REVERT: D 895 MET cc_start: 0.8793 (ptt) cc_final: 0.8025 (ppp) REVERT: D 1035 TYR cc_start: 0.7480 (t80) cc_final: 0.6952 (t80) REVERT: D 1050 LEU cc_start: 0.9191 (pt) cc_final: 0.8747 (tp) REVERT: D 1051 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7669 (ptp-170) REVERT: D 1477 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7636 (m-70) REVERT: D 2732 TRP cc_start: 0.7712 (t60) cc_final: 0.7476 (t60) REVERT: D 2793 ARG cc_start: 0.7371 (mmm160) cc_final: 0.6535 (mmm160) REVERT: D 3130 CYS cc_start: 0.8427 (m) cc_final: 0.7978 (m) REVERT: D 3220 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8376 (mm-30) REVERT: D 3235 MET cc_start: 0.7724 (pmm) cc_final: 0.6921 (ppp) REVERT: D 3246 MET cc_start: 0.8859 (mtp) cc_final: 0.8637 (mtt) REVERT: D 3314 LEU cc_start: 0.9389 (mm) cc_final: 0.9100 (mm) REVERT: D 3854 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8284 (t80) REVERT: D 4558 HIS cc_start: 0.7594 (m90) cc_final: 0.7325 (m-70) outliers start: 62 outliers final: 32 residues processed: 974 average time/residue: 2.0790 time to fit residues: 2926.7878 Evaluate side-chains 955 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 915 time to evaluate : 11.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1933 VAL Chi-restraints excluded: chain A residue 2480 VAL Chi-restraints excluded: chain A residue 2688 MET Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain B residue 1183 LEU Chi-restraints excluded: chain B residue 2444 THR Chi-restraints excluded: chain B residue 3022 PHE Chi-restraints excluded: chain B residue 3149 GLU Chi-restraints excluded: chain B residue 3166 PHE Chi-restraints excluded: chain B residue 3680 CYS Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain C residue 1183 LEU Chi-restraints excluded: chain C residue 1477 HIS Chi-restraints excluded: chain C residue 1835 HIS Chi-restraints excluded: chain C residue 1933 VAL Chi-restraints excluded: chain C residue 2480 VAL Chi-restraints excluded: chain C residue 2688 MET Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3166 PHE Chi-restraints excluded: chain C residue 3255 GLU Chi-restraints excluded: chain C residue 4734 TYR Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1477 HIS Chi-restraints excluded: chain D residue 1933 VAL Chi-restraints excluded: chain D residue 2173 GLU Chi-restraints excluded: chain D residue 2480 VAL Chi-restraints excluded: chain D residue 3166 PHE Chi-restraints excluded: chain D residue 3180 ILE Chi-restraints excluded: chain D residue 3854 PHE Chi-restraints excluded: chain D residue 4734 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 0.2980 chunk 1460 optimal weight: 5.9990 chunk 419 optimal weight: 9.9990 chunk 1264 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 380 optimal weight: 9.9990 chunk 1373 optimal weight: 3.9990 chunk 574 optimal weight: 8.9990 chunk 1409 optimal weight: 50.0000 chunk 173 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3034 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN F 44 ASN G 44 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3634 HIS ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4933 HIS ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2802 ASN ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.057310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043448 restraints weight = 1070353.078| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.69 r_work: 0.2999 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 141708 Z= 0.340 Angle : 0.667 19.831 191468 Z= 0.329 Chirality : 0.043 0.729 20988 Planarity : 0.004 0.072 24596 Dihedral : 5.889 112.742 19106 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 0.45 % Allowed : 11.02 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.08 (0.07), residues: 17212 helix: 1.90 (0.06), residues: 8908 sheet: -0.26 (0.13), residues: 1696 loop : -0.64 (0.08), residues: 6608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A3250 HIS 0.010 0.001 HIS B3700 PHE 0.033 0.002 PHE B4048 TYR 0.051 0.002 TYR A 931 ARG 0.015 0.001 ARG D2793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46647.98 seconds wall clock time: 809 minutes 52.50 seconds (48592.50 seconds total)