Starting phenix.real_space_refine on Sun Mar 10 14:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8duj_27721/03_2024/8duj_27721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8duj_27721/03_2024/8duj_27721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8duj_27721/03_2024/8duj_27721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8duj_27721/03_2024/8duj_27721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8duj_27721/03_2024/8duj_27721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8duj_27721/03_2024/8duj_27721_updated.pdb" } resolution = 3.7 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= 0.011 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 12 5.49 5 S 481 5.16 5 C 67549 2.51 5 N 19112 2.21 5 O 18994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1596": "OE1" <-> "OE2" Residue "G GLU 1733": "OE1" <-> "OE2" Residue "G GLU 3928": "OE1" <-> "OE2" Residue "G GLU 3967": "OE1" <-> "OE2" Residue "G GLU 4942": "OE1" <-> "OE2" Residue "G GLU 4948": "OE1" <-> "OE2" Residue "G GLU 4955": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "A PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3967": "OE1" <-> "OE2" Residue "A PHE 4061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4232": "OE1" <-> "OE2" Residue "A TYR 4795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4942": "OE1" <-> "OE2" Residue "A GLU 5007": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "D GLU 3928": "OE1" <-> "OE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J GLU 1733": "OE1" <-> "OE2" Residue "J TYR 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1835": "OE1" <-> "OE2" Residue "J GLU 4196": "OE1" <-> "OE2" Residue "J GLU 4900": "OE1" <-> "OE2" Residue "J GLU 4952": "OE1" <-> "OE2" Time to flip residues: 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 106156 Number of models: 1 Model: "" Number of chains: 17 Chain: "M" Number of atoms: 514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 33, 257 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Conformer: "B" Number of residues, atoms: 33, 257 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 26285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3933, 26285 Classifications: {'peptide': 3933} Incomplete info: {'truncation_to_alanine': 1473} Link IDs: {'PTRANS': 174, 'TRANS': 3758} Chain breaks: 52 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 5444 Unresolved non-hydrogen angles: 6804 Unresolved non-hydrogen dihedrals: 4427 Unresolved non-hydrogen chiralities: 353 Planarities with less than four sites: {'GLN:plan1': 85, 'ASP:plan': 140, 'TYR:plan': 29, 'ASN:plan1': 63, 'TRP:plan': 12, 'HIS:plan': 38, 'PHE:plan': 33, 'GLU:plan': 259, 'ARG:plan': 141} Unresolved non-hydrogen planarities: 3389 Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 759 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 711 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 224 Chain: "A" Number of atoms: 24845 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3823, 24843 Classifications: {'peptide': 3823} Incomplete info: {'truncation_to_alanine': 1617} Link IDs: {'PTRANS': 165, 'TRANS': 3657} Chain breaks: 52 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 6011 Unresolved non-hydrogen angles: 7509 Unresolved non-hydrogen dihedrals: 4880 Unresolved non-hydrogen chiralities: 410 Planarities with less than four sites: {'GLN:plan1': 104, 'HIS:plan': 33, 'TYR:plan': 28, 'ASN:plan1': 66, 'TRP:plan': 14, 'ASP:plan': 145, 'PHE:plan': 46, 'GLU:plan': 277, 'ARG:plan': 157} Unresolved non-hydrogen planarities: 3705 Conformer: "B" Number of residues, atoms: 3823, 24843 Classifications: {'peptide': 3823} Incomplete info: {'truncation_to_alanine': 1617} Link IDs: {'PTRANS': 165, 'TRANS': 3657} Chain breaks: 52 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 6011 Unresolved non-hydrogen angles: 7509 Unresolved non-hydrogen dihedrals: 4880 Unresolved non-hydrogen chiralities: 410 Planarities with less than four sites: {'GLN:plan1': 104, 'HIS:plan': 33, 'TYR:plan': 28, 'ASN:plan1': 66, 'TRP:plan': 14, 'ASP:plan': 145, 'PHE:plan': 46, 'GLU:plan': 277, 'ARG:plan': 157} Unresolved non-hydrogen planarities: 3705 bond proxies already assigned to first conformer: 25334 Chain: "B" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 735 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 707 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 2, 'TRANS': 134} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 228 Chain: "D" Number of atoms: 23336 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3865, 23334 Classifications: {'peptide': 3865} Incomplete info: {'truncation_to_alanine': 2189} Link IDs: {'PTRANS': 168, 'TRANS': 3696} Chain breaks: 57 Unresolved chain link angles: 69 Unresolved non-hydrogen bonds: 8028 Unresolved non-hydrogen angles: 10137 Unresolved non-hydrogen dihedrals: 6554 Unresolved non-hydrogen chiralities: 660 Planarities with less than four sites: {'GLN:plan1': 129, 'HIS:plan': 65, 'TYR:plan': 48, 'ASN:plan1': 85, 'TRP:plan': 20, 'ASP:plan': 165, 'PHE:plan': 76, 'GLU:plan': 279, 'ARG:plan': 196} Unresolved non-hydrogen planarities: 4659 Conformer: "B" Number of residues, atoms: 3865, 23334 Classifications: {'peptide': 3865} Incomplete info: {'truncation_to_alanine': 2189} Link IDs: {'PTRANS': 168, 'TRANS': 3696} Chain breaks: 57 Unresolved chain link angles: 69 Unresolved non-hydrogen bonds: 8028 Unresolved non-hydrogen angles: 10137 Unresolved non-hydrogen dihedrals: 6554 Unresolved non-hydrogen chiralities: 660 Planarities with less than four sites: {'GLN:plan1': 129, 'HIS:plan': 65, 'TYR:plan': 48, 'ASN:plan1': 85, 'TRP:plan': 20, 'ASP:plan': 165, 'PHE:plan': 76, 'GLU:plan': 279, 'ARG:plan': 196} Unresolved non-hydrogen planarities: 4659 bond proxies already assigned to first conformer: 23690 Chain: "E" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 657 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "F" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 710 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 2, 'TRANS': 134} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 469 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 222 Chain: "J" Number of atoms: 25245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3892, 25245 Classifications: {'peptide': 3892} Incomplete info: {'truncation_to_alanine': 1682} Link IDs: {'PTRANS': 170, 'TRANS': 3721} Chain breaks: 52 Unresolved chain link angles: 34 Unresolved non-hydrogen bonds: 6192 Unresolved non-hydrogen angles: 7788 Unresolved non-hydrogen dihedrals: 5026 Unresolved non-hydrogen chiralities: 439 Planarities with less than four sites: {'GLN:plan1': 106, 'HIS:plan': 50, 'TYR:plan': 33, 'ASN:plan1': 78, 'TRP:plan': 17, 'ASP:plan': 159, 'PHE:plan': 39, 'GLU:plan': 266, 'ARG:plan': 152} Unresolved non-hydrogen planarities: 3827 Chain: "K" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 758 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 706 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 231 Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26157 SG CYS G4958 124.547 171.460 199.834 1.00 71.62 S ATOM 26182 SG CYS G4961 121.110 171.196 198.331 1.00 67.60 S ATOM 52507 SG CYS A4958 125.289 202.048 199.809 1.00 41.95 S ATOM 52532 SG CYS A4961 121.902 200.278 199.916 1.00 38.10 S ATOM 77284 SG CYS D4958 125.434 198.527 169.391 1.00 59.85 S ATOM 77309 SG CYS D4961 122.425 197.716 171.705 1.00 60.06 S ATOM A0308 SG CYS J4958 123.896 168.411 171.215 1.00 78.67 S ATOM A030X SG CYS J4961 121.683 171.631 171.411 1.00 80.30 S Residues with excluded nonbonded symmetry interactions: 33 residue: pdb=" N AGLY M 1 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY M 1 " occ=0.50 residue: pdb=" N AASP M 2 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP M 2 " occ=0.50 residue: pdb=" N ACYS M 3 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS M 3 " occ=0.50 residue: pdb=" N ALEU M 4 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU M 4 " occ=0.50 residue: pdb=" N APRO M 5 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO M 5 " occ=0.50 residue: pdb=" N AHIS M 6 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS M 6 " occ=0.50 residue: pdb=" N ALEU M 7 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU M 7 " occ=0.50 residue: pdb=" N ALYS M 8 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS M 8 " occ=0.50 residue: pdb=" N AARG M 9 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG M 9 " occ=0.50 residue: pdb=" N ACYS M 10 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS M 10 " occ=0.50 residue: pdb=" N ALYS M 11 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS M 11 " occ=0.50 residue: pdb=" N AALA M 12 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA M 12 " occ=0.50 ... (remaining 21 not shown) Time building chain proxies: 57.20, per 1000 atoms: 0.54 Number of scatterers: 106156 At special positions: 0 Unit cell: (209.72, 371.29, 368.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 481 16.00 P 12 15.00 O 18994 8.00 N 19112 7.00 C 67549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG ACYS M 3 " - pdb=" SG ACYS M 17 " distance=2.03 Simple disulfide: pdb=" SG ACYS M 10 " - pdb=" SG ACYS M 21 " distance=2.03 Simple disulfide: pdb=" SG ACYS M 16 " - pdb=" SG ACYS M 32 " distance=2.03 Simple disulfide: pdb=" SG BCYS M 3 " - pdb=" SG BCYS M 17 " distance=2.03 Simple disulfide: pdb=" SG BCYS M 10 " - pdb=" SG BCYS M 21 " distance=2.03 Simple disulfide: pdb=" SG BCYS M 16 " - pdb=" SG BCYS M 32 " distance=2.03 Simple disulfide: pdb=" SG CYS G2310 " - pdb=" SG CYS G2326 " distance=2.03 Simple disulfide: pdb=" SG CYS G4876 " - pdb=" SG CYS G4882 " distance=2.03 Simple disulfide: pdb=" SG CYS A2310 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D2310 " - pdb=" SG CYS D2326 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Simple disulfide: pdb=" SG CYS J 36 " - pdb=" SG CYS J 65 " distance=2.03 Simple disulfide: pdb=" SG CYS J2310 " - pdb=" SG CYS J2326 " distance=2.03 Simple disulfide: pdb=" SG CYS J4876 " - pdb=" SG CYS J4882 " 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=0, symmetry=0 Time building additional restraints: 32.35 Conformation dependent library (CDL) restraints added in 23.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5104 " pdb="ZN ZN A5104 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5104 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5104 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5104 " - pdb=" SG CYS A4958 " pdb=" ZN D5104 " pdb="ZN ZN D5104 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5104 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5104 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5104 " - pdb=" SG CYS D4958 " pdb=" ZN G5104 " pdb="ZN ZN G5104 " - pdb=" ND1 HIS G4983 " pdb="ZN ZN G5104 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G5104 " - pdb=" SG CYS G4958 " pdb="ZN ZN G5104 " - pdb=" SG CYS G4961 " pdb=" ZN J5104 " pdb="ZN ZN J5104 " - pdb=" NE2 HIS J4978 " pdb="ZN ZN J5104 " - pdb=" ND1 HIS J4983 " pdb="ZN ZN J5104 " - pdb=" SG CYS J4958 " pdb="ZN ZN J5104 " - pdb=" SG CYS J4961 " Number of angles added : 6 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31198 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: 670 helices and 83 sheets defined 62.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 54.45 Creating SS restraints... Processing helix chain 'G' and resid 51 through 56 removed outlier: 4.849A pdb=" N ALA G 55 " --> pdb=" O PRO G 51 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLN G 56 " --> pdb=" O THR G 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 51 through 56' Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.585A pdb=" N CYS G 65 " --> pdb=" O ASP G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 84 Processing helix chain 'G' and resid 143 through 148 removed outlier: 4.533A pdb=" N TRP G 147 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 143 through 148' Processing helix chain 'G' and resid 250 through 256 removed outlier: 4.919A pdb=" N ALA G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 313 Processing helix chain 'G' and resid 394 through 422 removed outlier: 3.826A pdb=" N PHE G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 453 Processing helix chain 'G' and resid 466 through 482 removed outlier: 3.676A pdb=" N SER G 470 " --> pdb=" O SER G 466 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY G 482 " --> pdb=" O PHE G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 483 through 496 removed outlier: 3.942A pdb=" N VAL G 496 " --> pdb=" O ASP G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 532 removed outlier: 5.119A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 531 " --> pdb=" O ALA G 527 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY G 532 " --> pdb=" O SER G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 544 removed outlier: 4.419A pdb=" N THR G 542 " --> pdb=" O ALA G 538 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN G 543 " --> pdb=" O LEU G 539 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU G 544 " --> pdb=" O PHE G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 553 removed outlier: 3.809A pdb=" N ASP G 552 " --> pdb=" O VAL G 548 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG G 553 " --> pdb=" O SER G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 571 removed outlier: 3.635A pdb=" N ILE G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 578 removed outlier: 4.736A pdb=" N ASN G 576 " --> pdb=" O PRO G 572 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE G 577 " --> pdb=" O GLU G 573 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE G 578 " --> pdb=" O VAL G 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 572 through 578' Processing helix chain 'G' and resid 579 through 593 Processing helix chain 'G' and resid 596 through 609 removed outlier: 3.817A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP G 601 " --> pdb=" O HIS G 597 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS G 607 " --> pdb=" O LEU G 603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N CYS G 609 " --> pdb=" O SER G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 629 removed outlier: 3.777A pdb=" N GLN G 618 " --> pdb=" O VAL G 614 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 625 " --> pdb=" O ILE G 621 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU G 626 " --> pdb=" O THR G 622 " (cutoff:3.500A) Proline residue: G 627 - end of helix Processing helix chain 'G' and resid 810 through 815 removed outlier: 4.742A pdb=" N ALA G 814 " --> pdb=" O PRO G 810 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL G 815 " --> pdb=" O CYS G 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 810 through 815' Processing helix chain 'G' and resid 847 through 853 Proline residue: G 853 - end of helix Processing helix chain 'G' and resid 865 through 887 removed outlier: 3.759A pdb=" N ILE G 870 " --> pdb=" O HIS G 866 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 936 removed outlier: 3.795A pdb=" N GLY G 936 " --> pdb=" O LEU G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 956 through 961 removed outlier: 5.115A pdb=" N MET G 961 " --> pdb=" O LYS G 957 " (cutoff:3.500A) Processing helix chain 'G' and resid 971 through 976 removed outlier: 5.085A pdb=" N ARG G 976 " --> pdb=" O LEU G 972 " (cutoff:3.500A) Processing helix chain 'G' and resid 979 through 1004 removed outlier: 5.080A pdb=" N THR G 983 " --> pdb=" O PRO G 979 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU G 984 " --> pdb=" O ALA G 980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1050 Processing helix chain 'G' and resid 1207 through 1212 removed outlier: 5.093A pdb=" N ARG G1212 " --> pdb=" O VAL G1208 " (cutoff:3.500A) Processing helix chain 'G' and resid 1213 through 1218 removed outlier: 3.881A pdb=" N GLY G1218 " --> pdb=" O PHE G1214 " (cutoff:3.500A) Processing helix chain 'G' and resid 1444 through 1449 removed outlier: 3.866A pdb=" N VAL G1448 " --> pdb=" O GLU G1444 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP G1449 " --> pdb=" O PRO G1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1444 through 1449' Processing helix chain 'G' and resid 1496 through 1501 Processing helix chain 'G' and resid 1574 through 1581 removed outlier: 3.864A pdb=" N ALA G1578 " --> pdb=" O PRO G1574 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU G1581 " --> pdb=" O ALA G1577 " (cutoff:3.500A) Processing helix chain 'G' and resid 1652 through 1657 removed outlier: 3.795A pdb=" N ARG G1656 " --> pdb=" O GLU G1652 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1652 through 1657' Processing helix chain 'G' and resid 1658 through 1675 Processing helix chain 'G' and resid 1678 through 1690 removed outlier: 3.681A pdb=" N SER G1687 " --> pdb=" O HIS G1683 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS G1688 " --> pdb=" O ALA G1684 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP G1690 " --> pdb=" O CYS G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1691 through 1700 Processing helix chain 'G' and resid 1704 through 1719 Processing helix chain 'G' and resid 1720 through 1732 removed outlier: 4.174A pdb=" N SER G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1745 removed outlier: 3.928A pdb=" N ALA G1744 " --> pdb=" O PRO G1740 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE G1745 " --> pdb=" O GLU G1741 " (cutoff:3.500A) Processing helix chain 'G' and resid 1803 through 1825 removed outlier: 6.448A pdb=" N LEU G1807 " --> pdb=" O PRO G1803 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG G1808 " --> pdb=" O LEU G1804 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1852 Proline residue: G1840 - end of helix removed outlier: 3.565A pdb=" N GLY G1852 " --> pdb=" O LEU G1848 " (cutoff:3.500A) Processing helix chain 'G' and resid 1855 through 1867 Processing helix chain 'G' and resid 1925 through 1930 removed outlier: 3.707A pdb=" N MET G1929 " --> pdb=" O GLY G1925 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS G1930 " --> pdb=" O LEU G1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1925 through 1930' Processing helix chain 'G' and resid 1932 through 1984 removed outlier: 3.903A pdb=" N ASP G1967 " --> pdb=" O GLU G1963 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS G1968 " --> pdb=" O ARG G1964 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE G1984 " --> pdb=" O LEU G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1987 through 1998 removed outlier: 3.592A pdb=" N ARG G1996 " --> pdb=" O ALA G1992 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE G1998 " --> pdb=" O ARG G1994 " (cutoff:3.500A) Processing helix chain 'G' and resid 2001 through 2011 removed outlier: 3.793A pdb=" N HIS G2011 " --> pdb=" O ASN G2007 " (cutoff:3.500A) Processing helix chain 'G' and resid 2024 through 2043 removed outlier: 3.504A pdb=" N ARG G2028 " --> pdb=" O PRO G2024 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY G2043 " --> pdb=" O LEU G2039 " (cutoff:3.500A) Processing helix chain 'G' and resid 2093 through 2109 removed outlier: 4.003A pdb=" N ASP G2109 " --> pdb=" O TRP G2105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2130 removed outlier: 3.942A pdb=" N GLY G2130 " --> pdb=" O ARG G2126 " (cutoff:3.500A) Processing helix chain 'G' and resid 2131 through 2142 Proline residue: G2139 - end of helix removed outlier: 5.428A pdb=" N TYR G2142 " --> pdb=" O LEU G2138 " (cutoff:3.500A) Processing helix chain 'G' and resid 2148 through 2169 removed outlier: 3.740A pdb=" N ILE G2167 " --> pdb=" O ARG G2163 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G2168 " --> pdb=" O SER G2164 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN G2169 " --> pdb=" O LEU G2165 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2189 removed outlier: 5.517A pdb=" N LYS G2189 " --> pdb=" O ILE G2185 " (cutoff:3.500A) Processing helix chain 'G' and resid 2194 through 2202 removed outlier: 3.882A pdb=" N MET G2198 " --> pdb=" O HIS G2194 " (cutoff:3.500A) Processing helix chain 'G' and resid 2203 through 2216 Processing helix chain 'G' and resid 2225 through 2244 removed outlier: 4.039A pdb=" N SER G2243 " --> pdb=" O PHE G2239 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG G2244 " --> pdb=" O CYS G2240 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2255 removed outlier: 4.301A pdb=" N HIS G2253 " --> pdb=" O SER G2249 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G2254 " --> pdb=" O MET G2250 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER G2255 " --> pdb=" O PHE G2251 " (cutoff:3.500A) Processing helix chain 'G' and resid 2256 through 2261 removed outlier: 3.857A pdb=" N SER G2261 " --> pdb=" O LEU G2257 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2281 Processing helix chain 'G' and resid 2283 through 2290 Processing helix chain 'G' and resid 2291 through 2309 removed outlier: 3.738A pdb=" N LEU G2295 " --> pdb=" O GLN G2291 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU G2307 " --> pdb=" O ALA G2303 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN G2308 " --> pdb=" O GLY G2304 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER G2309 " --> pdb=" O CYS G2305 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2317 Processing helix chain 'G' and resid 2324 through 2341 removed outlier: 3.695A pdb=" N GLY G2328 " --> pdb=" O ASN G2324 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG G2330 " --> pdb=" O CYS G2326 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL G2341 " --> pdb=" O PHE G2337 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2361 removed outlier: 3.739A pdb=" N LYS G2360 " --> pdb=" O LEU G2356 " (cutoff:3.500A) Proline residue: G2361 - end of helix Processing helix chain 'G' and resid 2375 through 2390 Proline residue: G2390 - end of helix Processing helix chain 'G' and resid 2417 through 2437 removed outlier: 3.592A pdb=" N ALA G2437 " --> pdb=" O LEU G2433 " (cutoff:3.500A) Processing helix chain 'G' and resid 2439 through 2446 removed outlier: 3.542A pdb=" N GLY G2446 " --> pdb=" O LEU G2442 " (cutoff:3.500A) Processing helix chain 'G' and resid 2447 through 2462 Proline residue: G2462 - end of helix Processing helix chain 'G' and resid 2463 through 2472 Processing helix chain 'G' and resid 2495 through 2509 removed outlier: 4.419A pdb=" N LYS G2499 " --> pdb=" O VAL G2495 " (cutoff:3.500A) Processing helix chain 'G' and resid 2514 through 2525 removed outlier: 3.558A pdb=" N LEU G2518 " --> pdb=" O ASN G2514 " (cutoff:3.500A) Processing helix chain 'G' and resid 2526 through 2537 removed outlier: 3.961A pdb=" N MET G2530 " --> pdb=" O PHE G2526 " (cutoff:3.500A) Processing helix chain 'G' and resid 2544 through 2566 removed outlier: 4.533A pdb=" N LEU G2559 " --> pdb=" O CYS G2555 " (cutoff:3.500A) Proline residue: G2560 - end of helix Processing helix chain 'G' and resid 2575 through 2592 removed outlier: 4.554A pdb=" N GLY G2592 " --> pdb=" O ARG G2588 " (cutoff:3.500A) Processing helix chain 'G' and resid 2596 through 2614 removed outlier: 4.832A pdb=" N TYR G2613 " --> pdb=" O ALA G2609 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE G2614 " --> pdb=" O LEU G2610 " (cutoff:3.500A) Processing helix chain 'G' and resid 2615 through 2633 removed outlier: 4.502A pdb=" N LEU G2619 " --> pdb=" O ARG G2615 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN G2620 " --> pdb=" O PRO G2616 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N HIS G2621 " --> pdb=" O SER G2617 " (cutoff:3.500A) Proline residue: G2631 - end of helix Processing helix chain 'G' and resid 2637 through 2652 removed outlier: 4.662A pdb=" N LEU G2641 " --> pdb=" O ALA G2637 " (cutoff:3.500A) Processing helix chain 'G' and resid 2668 through 2689 removed outlier: 3.757A pdb=" N PHE G2683 " --> pdb=" O PHE G2679 " (cutoff:3.500A) Processing helix chain 'G' and resid 2693 through 2707 Proline residue: G2701 - end of helix Processing helix chain 'G' and resid 2748 through 2774 Processing helix chain 'G' and resid 2793 through 2798 removed outlier: 4.948A pdb=" N SER G2798 " --> pdb=" O TYR G2794 " (cutoff:3.500A) Processing helix chain 'G' and resid 2800 through 2820 Proline residue: G2808 - end of helix Processing helix chain 'G' and resid 2868 through 2898 Processing helix chain 'G' and resid 2912 through 2934 removed outlier: 4.483A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) Processing helix chain 'G' and resid 2951 through 2979 Processing helix chain 'G' and resid 2991 through 3014 removed outlier: 3.960A pdb=" N LEU G3002 " --> pdb=" O PHE G2998 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU G3003 " --> pdb=" O ALA G2999 " (cutoff:3.500A) Proline residue: G3004 - end of helix Processing helix chain 'G' and resid 3033 through 3052 Processing helix chain 'G' and resid 3064 through 3073 Processing helix chain 'G' and resid 3089 through 3111 Processing helix chain 'G' and resid 3127 through 3150 Proline residue: G3138 - end of helix Processing helix chain 'G' and resid 3160 through 3175 Processing helix chain 'G' and resid 3187 through 3199 Processing helix chain 'G' and resid 3248 through 3257 Processing helix chain 'G' and resid 3267 through 3284 removed outlier: 4.359A pdb=" N GLU G3271 " --> pdb=" O PRO G3267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE G3272 " --> pdb=" O HIS G3268 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU G3274 " --> pdb=" O ILE G3270 " (cutoff:3.500A) Proline residue: G3275 - end of helix Proline residue: G3282 - end of helix Processing helix chain 'G' and resid 3309 through 3326 Processing helix chain 'G' and resid 3337 through 3343 removed outlier: 4.008A pdb=" N GLN G3343 " --> pdb=" O ALA G3339 " (cutoff:3.500A) Processing helix chain 'G' and resid 3350 through 3379 removed outlier: 3.680A pdb=" N LEU G3354 " --> pdb=" O ARG G3350 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE G3359 " --> pdb=" O HIS G3355 " (cutoff:3.500A) Proline residue: G3360 - end of helix Processing helix chain 'G' and resid 3395 through 3421 Proline residue: G3410 - end of helix Processing helix chain 'G' and resid 3428 through 3449 removed outlier: 4.665A pdb=" N HIS G3449 " --> pdb=" O TRP G3445 " (cutoff:3.500A) Processing helix chain 'G' and resid 3450 through 3463 Processing helix chain 'G' and resid 3510 through 3525 Proline residue: G3519 - end of helix removed outlier: 4.382A pdb=" N CYS G3525 " --> pdb=" O GLY G3521 " (cutoff:3.500A) Processing helix chain 'G' and resid 3530 through 3543 Processing helix chain 'G' and resid 3545 through 3555 removed outlier: 3.957A pdb=" N VAL G3549 " --> pdb=" O THR G3545 " (cutoff:3.500A) Processing helix chain 'G' and resid 3590 through 3611 removed outlier: 4.540A pdb=" N ARG G3594 " --> pdb=" O GLU G3590 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG G3595 " --> pdb=" O LYS G3591 " (cutoff:3.500A) Processing helix chain 'G' and resid 3625 through 3638 removed outlier: 3.524A pdb=" N ARG G3629 " --> pdb=" O SER G3625 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE G3636 " --> pdb=" O VAL G3632 " (cutoff:3.500A) Processing helix chain 'G' and resid 3640 through 3645 removed outlier: 3.822A pdb=" N LEU G3644 " --> pdb=" O PRO G3640 " (cutoff:3.500A) Proline residue: G3645 - end of helix No H-bonds generated for 'chain 'G' and resid 3640 through 3645' Processing helix chain 'G' and resid 3646 through 3665 removed outlier: 4.620A pdb=" N ILE G3662 " --> pdb=" O LYS G3658 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU G3663 " --> pdb=" O ALA G3659 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR G3664 " --> pdb=" O ALA G3660 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU G3665 " --> pdb=" O TRP G3661 " (cutoff:3.500A) Processing helix chain 'G' and resid 3668 through 3680 removed outlier: 4.013A pdb=" N ARG G3672 " --> pdb=" O SER G3668 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA G3680 " --> pdb=" O ASP G3676 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3711 removed outlier: 3.574A pdb=" N THR G3711 " --> pdb=" O ARG G3707 " (cutoff:3.500A) Processing helix chain 'G' and resid 3719 through 3735 Processing helix chain 'G' and resid 3752 through 3772 removed outlier: 3.945A pdb=" N LEU G3770 " --> pdb=" O GLN G3766 " (cutoff:3.500A) Processing helix chain 'G' and resid 3774 through 3787 removed outlier: 4.527A pdb=" N LYS G3787 " --> pdb=" O ILE G3783 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3806 Processing helix chain 'G' and resid 3809 through 3824 Processing helix chain 'G' and resid 3826 through 3840 removed outlier: 6.051A pdb=" N SER G3840 " --> pdb=" O MET G3836 " (cutoff:3.500A) Processing helix chain 'G' and resid 3843 through 3857 removed outlier: 5.234A pdb=" N GLY G3857 " --> pdb=" O ALA G3853 " (cutoff:3.500A) Processing helix chain 'G' and resid 3877 through 3893 removed outlier: 3.742A pdb=" N CYS G3892 " --> pdb=" O LEU G3888 " (cutoff:3.500A) Processing helix chain 'G' and resid 3896 through 3905 Processing helix chain 'G' and resid 3914 through 3941 removed outlier: 3.966A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY G3939 " --> pdb=" O TRP G3935 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS G3940 " --> pdb=" O TYR G3936 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3970 Processing helix chain 'G' and resid 3973 through 3983 Processing helix chain 'G' and resid 3984 through 4007 removed outlier: 3.664A pdb=" N ALA G3988 " --> pdb=" O ARG G3984 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER G4007 " --> pdb=" O LEU G4003 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4032 Processing helix chain 'G' and resid 4038 through 4052 removed outlier: 3.548A pdb=" N ARG G4042 " --> pdb=" O GLY G4038 " (cutoff:3.500A) Processing helix chain 'G' and resid 4053 through 4075 removed outlier: 3.857A pdb=" N GLY G4073 " --> pdb=" O LYS G4069 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU G4075 " --> pdb=" O ILE G4071 " (cutoff:3.500A) Processing helix chain 'G' and resid 4076 through 4081 removed outlier: 4.094A pdb=" N TYR G4080 " --> pdb=" O ALA G4076 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL G4081 " --> pdb=" O PHE G4077 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4076 through 4081' Processing helix chain 'G' and resid 4089 through 4101 Processing helix chain 'G' and resid 4104 through 4116 removed outlier: 5.291A pdb=" N GLU G4116 " --> pdb=" O LEU G4112 " (cutoff:3.500A) Processing helix chain 'G' and resid 4134 through 4155 removed outlier: 4.742A pdb=" N ASP G4138 " --> pdb=" O GLU G4134 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE G4139 " --> pdb=" O PRO G4135 " (cutoff:3.500A) Proline residue: G4155 - end of helix Processing helix chain 'G' and resid 4157 through 4168 removed outlier: 3.554A pdb=" N ALA G4167 " --> pdb=" O PHE G4163 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU G4168 " --> pdb=" O LEU G4164 " (cutoff:3.500A) Processing helix chain 'G' and resid 4169 through 4175 Processing helix chain 'G' and resid 4198 through 4207 removed outlier: 3.570A pdb=" N ARG G4202 " --> pdb=" O SER G4198 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET G4207 " --> pdb=" O ALA G4203 " (cutoff:3.500A) Processing helix chain 'G' and resid 4208 through 4225 Processing helix chain 'G' and resid 4229 through 4252 Processing helix chain 'G' and resid 4323 through 4341 removed outlier: 3.675A pdb=" N ALA G4327 " --> pdb=" O THR G4323 " (cutoff:3.500A) Processing helix chain 'G' and resid 4541 through 4559 Processing helix chain 'G' and resid 4560 through 4580 removed outlier: 4.236A pdb=" N PHE G4579 " --> pdb=" O PHE G4575 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR G4580 " --> pdb=" O ILE G4576 " (cutoff:3.500A) Processing helix chain 'G' and resid 4638 through 4683 removed outlier: 3.975A pdb=" N VAL G4666 " --> pdb=" O ASN G4662 " (cutoff:3.500A) Proline residue: G4667 - end of helix Processing helix chain 'G' and resid 4696 through 4709 removed outlier: 4.367A pdb=" N ASN G4707 " --> pdb=" O ARG G4703 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR G4708 " --> pdb=" O LEU G4704 " (cutoff:3.500A) Proline residue: G4709 - end of helix Processing helix chain 'G' and resid 4719 through 4728 Processing helix chain 'G' and resid 4733 through 4742 removed outlier: 3.830A pdb=" N ALA G4738 " --> pdb=" O ARG G4734 " (cutoff:3.500A) Processing helix chain 'G' and resid 4745 through 4755 Processing helix chain 'G' and resid 4766 through 4772 removed outlier: 5.535A pdb=" N ASP G4772 " --> pdb=" O LEU G4768 " (cutoff:3.500A) Processing helix chain 'G' and resid 4773 through 4786 removed outlier: 3.789A pdb=" N ASP G4786 " --> pdb=" O VAL G4782 " (cutoff:3.500A) Processing helix chain 'G' and resid 4787 through 4806 Processing helix chain 'G' and resid 4809 through 4821 removed outlier: 4.542A pdb=" N LEU G4813 " --> pdb=" O PHE G4809 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU G4814 " --> pdb=" O ALA G4810 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP G4815 " --> pdb=" O ALA G4811 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE G4816 " --> pdb=" O HIS G4812 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA G4817 " --> pdb=" O LEU G4813 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET G4818 " --> pdb=" O LEU G4814 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL G4820 " --> pdb=" O ILE G4816 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS G4821 " --> pdb=" O ALA G4817 " (cutoff:3.500A) Processing helix chain 'G' and resid 4822 through 4832 removed outlier: 3.519A pdb=" N THR G4831 " --> pdb=" O LEU G4827 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4858 Processing helix chain 'G' and resid 4859 through 4864 removed outlier: 4.011A pdb=" N TYR G4863 " --> pdb=" O PHE G4859 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN G4864 " --> pdb=" O ARG G4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 4859 through 4864' Processing helix chain 'G' and resid 4878 through 4893 removed outlier: 4.907A pdb=" N VAL G4891 " --> pdb=" O MET G4887 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG G4892 " --> pdb=" O TYR G4888 " (cutoff:3.500A) Processing helix chain 'G' and resid 4897 through 4902 removed outlier: 5.187A pdb=" N GLU G4902 " --> pdb=" O GLY G4898 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4924 Processing helix chain 'G' and resid 4928 through 4957 removed outlier: 3.723A pdb=" N LYS G4951 " --> pdb=" O GLN G4947 " (cutoff:3.500A) Processing helix chain 'G' and resid 4964 through 4970 removed outlier: 4.033A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR G4970 " --> pdb=" O ASP G4966 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4981 Processing helix chain 'G' and resid 4984 through 4999 removed outlier: 5.001A pdb=" N ASP G4999 " --> pdb=" O LEU G4995 " (cutoff:3.500A) Processing helix chain 'G' and resid 5004 through 5017 Processing helix chain 'G' and resid 5027 through 5033 Processing helix chain 'H' and resid 38 through 43 removed outlier: 4.652A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 38 through 43' Processing helix chain 'H' and resid 56 through 66 Processing helix chain 'H' and resid 77 through 82 removed outlier: 4.163A pdb=" N TYR H 82 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.626A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 Processing helix chain 'B' and resid 77 through 82 removed outlier: 5.408A pdb=" N TYR B 82 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'I' and resid 6 through 21 Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 65 through 95 removed outlier: 4.661A pdb=" N SER I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU I 83 " --> pdb=" O ASP I 79 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU I 84 " --> pdb=" O THR I 80 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 95 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'A' and resid 61 through 66 removed outlier: 5.573A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.754A pdb=" N TRP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 148' Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.556A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 394 through 423 removed outlier: 5.213A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.991A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.875A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.384A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.640A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLY A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 542 removed outlier: 4.303A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.917A pdb=" N ASP A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.854A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.151A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.510A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 3.569A pdb=" N THR A 622 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Proline residue: A 627 - end of helix Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.548A pdb=" N ALA A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 815' Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.586A pdb=" N PHE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Proline residue: A 853 - end of helix Processing helix chain 'A' and resid 864 through 886 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.963A pdb=" N ASN A 909 " --> pdb=" O PRO A 905 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A 910 " --> pdb=" O CYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 removed outlier: 3.550A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1004 Processing helix chain 'A' and resid 1028 through 1050 removed outlier: 3.739A pdb=" N GLY A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1212 removed outlier: 3.542A pdb=" N LEU A1211 " --> pdb=" O ASP A1207 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG A1212 " --> pdb=" O VAL A1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1207 through 1212' Processing helix chain 'A' and resid 1215 through 1222 removed outlier: 4.766A pdb=" N LEU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 3.774A pdb=" N VAL A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TRP A1449 " --> pdb=" O PRO A1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1444 through 1449' Processing helix chain 'A' and resid 1496 through 1501 Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 3.924A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 3.748A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1657' Processing helix chain 'A' and resid 1658 through 1675 Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 3.586A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 removed outlier: 5.112A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1720 Processing helix chain 'A' and resid 1721 through 1732 removed outlier: 4.103A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1746 removed outlier: 5.597A pdb=" N THR A1746 " --> pdb=" O THR A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix removed outlier: 3.649A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1868 removed outlier: 3.748A pdb=" N GLU A1867 " --> pdb=" O LEU A1863 " (cutoff:3.500A) Proline residue: A1868 - end of helix Processing helix chain 'A' and resid 1932 through 1984 removed outlier: 4.081A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1998 removed outlier: 3.809A pdb=" N ARG A1996 " --> pdb=" O ALA A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2012 removed outlier: 3.896A pdb=" N PHE A2012 " --> pdb=" O MET A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 4.984A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.930A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.816A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 4.952A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.763A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2189 removed outlier: 6.820A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS A2189 " --> pdb=" O ILE A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2195 Proline residue: A2195 - end of helix Processing helix chain 'A' and resid 2196 through 2202 removed outlier: 3.880A pdb=" N GLY A2202 " --> pdb=" O MET A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2216 Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 4.232A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 3.983A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2261 Processing helix chain 'A' and resid 2271 through 2281 Processing helix chain 'A' and resid 2283 through 2291 removed outlier: 5.781A pdb=" N GLN A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2292 through 2309 removed outlier: 4.267A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A2308 " --> pdb=" O GLY A2304 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 Processing helix chain 'A' and resid 2324 through 2340 Processing helix chain 'A' and resid 2346 through 2361 Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 3.658A pdb=" N ALA A2421 " --> pdb=" O HIS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2446 Processing helix chain 'A' and resid 2447 through 2462 Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2463 through 2472 Processing helix chain 'A' and resid 2495 through 2510 removed outlier: 4.306A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2526 removed outlier: 4.543A pdb=" N GLY A2525 " --> pdb=" O VAL A2521 " (cutoff:3.500A) Processing helix chain 'A' and resid 2527 through 2537 Processing helix chain 'A' and resid 2544 through 2566 removed outlier: 5.107A pdb=" N LEU A2559 " --> pdb=" O CYS A2555 " (cutoff:3.500A) Proline residue: A2560 - end of helix Processing helix chain 'A' and resid 2575 through 2592 Processing helix chain 'A' and resid 2596 through 2614 removed outlier: 5.118A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2623 removed outlier: 3.558A pdb=" N LEU A2619 " --> pdb=" O ARG A2615 " (cutoff:3.500A) Processing helix chain 'A' and resid 2624 through 2636 Proline residue: A2631 - end of helix Processing helix chain 'A' and resid 2637 through 2650 Processing helix chain 'A' and resid 2669 through 2689 removed outlier: 3.565A pdb=" N HIS A2673 " --> pdb=" O GLU A2669 " (cutoff:3.500A) Processing helix chain 'A' and resid 2692 through 2700 Processing helix chain 'A' and resid 2749 through 2774 Processing helix chain 'A' and resid 2793 through 2798 removed outlier: 4.693A pdb=" N SER A2798 " --> pdb=" O TYR A2794 " (cutoff:3.500A) Processing helix chain 'A' and resid 2799 through 2820 Proline residue: A2808 - end of helix Processing helix chain 'A' and resid 2868 through 2898 Processing helix chain 'A' and resid 2912 through 2934 Processing helix chain 'A' and resid 2955 through 2974 Processing helix chain 'A' and resid 2994 through 3013 removed outlier: 3.829A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix Processing helix chain 'A' and resid 3035 through 3049 Processing helix chain 'A' and resid 3063 through 3073 Processing helix chain 'A' and resid 3086 through 3108 Processing helix chain 'A' and resid 3126 through 3149 Proline residue: A3138 - end of helix Processing helix chain 'A' and resid 3160 through 3177 Processing helix chain 'A' and resid 3188 through 3196 Processing helix chain 'A' and resid 3274 through 3285 Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3309 through 3326 Processing helix chain 'A' and resid 3335 through 3344 Proline residue: A3344 - end of helix Processing helix chain 'A' and resid 3356 through 3384 Proline residue: A3360 - end of helix removed outlier: 4.963A pdb=" N LYS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3421 removed outlier: 3.873A pdb=" N PHE A3398 " --> pdb=" O VAL A3394 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A3399 " --> pdb=" O ARG A3395 " (cutoff:3.500A) Proline residue: A3410 - end of helix Processing helix chain 'A' and resid 3428 through 3448 removed outlier: 3.851A pdb=" N SER A3448 " --> pdb=" O TYR A3444 " (cutoff:3.500A) Processing helix chain 'A' and resid 3449 through 3461 Processing helix chain 'A' and resid 3511 through 3523 removed outlier: 3.971A pdb=" N LYS A3515 " --> pdb=" O VAL A3511 " (cutoff:3.500A) Proline residue: A3519 - end of helix Processing helix chain 'A' and resid 3530 through 3543 removed outlier: 4.846A pdb=" N MET A3534 " --> pdb=" O GLN A3530 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A3535 " --> pdb=" O ASP A3531 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A3542 " --> pdb=" O THR A3538 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A3543 " --> pdb=" O ARG A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3546 through 3551 Processing helix chain 'A' and resid 3590 through 3611 Processing helix chain 'A' and resid 3625 through 3638 removed outlier: 4.124A pdb=" N ARG A3637 " --> pdb=" O VAL A3633 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N MET A3638 " --> pdb=" O ALA A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3645 removed outlier: 3.733A pdb=" N LEU A3644 " --> pdb=" O PRO A3640 " (cutoff:3.500A) Proline residue: A3645 - end of helix No H-bonds generated for 'chain 'A' and resid 3640 through 3645' Processing helix chain 'A' and resid 3646 through 3665 removed outlier: 4.485A pdb=" N ILE A3662 " --> pdb=" O LYS A3658 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU A3663 " --> pdb=" O ALA A3659 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A3664 " --> pdb=" O ALA A3660 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3679 removed outlier: 4.059A pdb=" N ARG A3672 " --> pdb=" O SER A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3712 removed outlier: 3.737A pdb=" N ALA A3709 " --> pdb=" O PHE A3705 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A3710 " --> pdb=" O SER A3706 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A3711 " --> pdb=" O ARG A3707 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU A3712 " --> pdb=" O THR A3708 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 3.697A pdb=" N MET A3723 " --> pdb=" O ASP A3719 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A3727 " --> pdb=" O MET A3723 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.819A pdb=" N MET A3778 " --> pdb=" O GLY A3774 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 3.535A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3856 removed outlier: 3.806A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3871 removed outlier: 3.898A pdb=" N GLN A3869 " --> pdb=" O VAL A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.776A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3906 Processing helix chain 'A' and resid 3914 through 3941 removed outlier: 3.747A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A3940 " --> pdb=" O TYR A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 5.110A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4007 removed outlier: 3.699A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER A4007 " --> pdb=" O LEU A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 3.512A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) Processing helix chain 'A' and resid 4053 through 4075 removed outlier: 4.783A pdb=" N GLU A4075 " --> pdb=" O ILE A4071 " (cutoff:3.500A) Processing helix chain 'A' and resid 4076 through 4081 Processing helix chain 'A' and resid 4089 through 4101 Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 4.896A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4137 removed outlier: 4.390A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix Processing helix chain 'A' and resid 4138 through 4154 Processing helix chain 'A' and resid 4157 through 4168 Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 3.870A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4225 Processing helix chain 'A' and resid 4229 through 4252 removed outlier: 3.548A pdb=" N LEU A4233 " --> pdb=" O GLU A4229 " (cutoff:3.500A) Processing helix chain 'A' and resid 4324 through 4341 removed outlier: 4.023A pdb=" N ALA A4328 " --> pdb=" O ALA A4324 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4559 Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 4.165A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4638 through 4683 removed outlier: 3.835A pdb=" N CYS A4663 " --> pdb=" O ILE A4659 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A4665 " --> pdb=" O TYR A4661 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix Processing helix chain 'A' and resid 4696 through 4709 removed outlier: 4.619A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR A4708 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Proline residue: A4709 - end of helix Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 4.927A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4742 removed outlier: 4.712A pdb=" N ALA A4738 " --> pdb=" O ARG A4734 " (cutoff:3.500A) Processing helix chain 'A' and resid 4745 through 4755 Processing helix chain 'A' and resid 4766 through 4771 Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 5.843A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4805 removed outlier: 3.920A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4820 removed outlier: 4.646A pdb=" N ALA A4810 " --> pdb=" O ASN A4806 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 4.282A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A4831 " --> pdb=" O LEU A4827 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.983A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4902 removed outlier: 5.023A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4928 through 4953 removed outlier: 3.739A pdb=" N LYS A4951 " --> pdb=" O GLN A4947 " (cutoff:3.500A) Processing helix chain 'A' and resid 4966 through 4972 removed outlier: 3.975A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR A4971 " --> pdb=" O TYR A4967 " (cutoff:3.500A) Proline residue: A4972 - end of helix No H-bonds generated for 'chain 'A' and resid 4966 through 4972' Processing helix chain 'A' and resid 4973 through 4981 removed outlier: 3.692A pdb=" N THR A4977 " --> pdb=" O HIS A4973 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A4979 " --> pdb=" O PHE A4975 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A4980 " --> pdb=" O GLU A4976 " (cutoff:3.500A) Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 5.079A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 removed outlier: 3.774A pdb=" N ARG A5017 " --> pdb=" O MET A5013 " (cutoff:3.500A) Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 4685 through 4690 Processing helix chain 'C' and resid 6 through 23 removed outlier: 4.674A pdb=" N LEU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 removed outlier: 3.638A pdb=" N GLY C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 65 through 94 removed outlier: 3.538A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.710A pdb=" N LEU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 removed outlier: 4.648A pdb=" N GLU C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N MET C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'F' and resid 6 through 22 removed outlier: 3.643A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 65 through 96 removed outlier: 4.568A pdb=" N ASP F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP F 96 " --> pdb=" O VAL F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.900A 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 250 through 256 removed outlier: 4.447A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 394 through 425 removed outlier: 4.315A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Proline residue: D 425 - end of helix Processing helix chain 'D' and resid 437 through 453 Processing helix chain 'D' and resid 465 through 482 removed outlier: 4.094A pdb=" N ARG D 469 " --> pdb=" O GLN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.705A pdb=" N TYR D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR D 498 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 533 removed outlier: 4.259A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 544 Processing helix chain 'D' and resid 545 through 553 removed outlier: 3.606A pdb=" N ARG D 553 " --> pdb=" O SER D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 572 removed outlier: 3.675A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Proline residue: D 572 - end of helix Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.906A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.677A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 629 removed outlier: 3.909A pdb=" N LEU D 625 " --> pdb=" O ILE D 621 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Proline residue: D 627 - end of helix Processing helix chain 'D' and resid 706 through 711 removed outlier: 5.500A pdb=" N LEU D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 815 removed outlier: 4.093A pdb=" N ALA D 814 " --> pdb=" O PRO D 810 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 815 " --> pdb=" O CYS D 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 815' Processing helix chain 'D' and resid 848 through 853 Proline residue: D 853 - end of helix Processing helix chain 'D' and resid 864 through 887 removed outlier: 4.008A pdb=" N ILE D 887 " --> pdb=" O ALA D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 909 removed outlier: 3.505A pdb=" N ASN D 909 " --> pdb=" O PRO D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 Processing helix chain 'D' and resid 946 through 951 removed outlier: 4.799A pdb=" N LEU D 950 " --> pdb=" O ALA D 946 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS D 951 " --> pdb=" O GLU D 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 946 through 951' Processing helix chain 'D' and resid 956 through 961 Processing helix chain 'D' and resid 971 through 976 removed outlier: 4.762A pdb=" N ARG D 976 " --> pdb=" O LEU D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 1004 Processing helix chain 'D' and resid 1028 through 1050 Processing helix chain 'D' and resid 1078 through 1083 removed outlier: 3.685A pdb=" N THR D1082 " --> pdb=" O GLU D1078 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1078 through 1083' Processing helix chain 'D' and resid 1207 through 1212 removed outlier: 3.753A pdb=" N LEU D1211 " --> pdb=" O ASP D1207 " (cutoff:3.500A) Processing helix chain 'D' and resid 1213 through 1222 Processing helix chain 'D' and resid 1225 through 1231 removed outlier: 4.777A pdb=" N ASN D1229 " --> pdb=" O PRO D1225 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET D1230 " --> pdb=" O PHE D1226 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN D1231 " --> pdb=" O ALA D1227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1225 through 1231' Processing helix chain 'D' and resid 1496 through 1501 Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 3.839A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 3.572A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1657' Processing helix chain 'D' and resid 1658 through 1675 Processing helix chain 'D' and resid 1678 through 1690 Processing helix chain 'D' and resid 1691 through 1701 removed outlier: 5.103A pdb=" N LEU D1695 " --> pdb=" O GLN D1691 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1718 removed outlier: 3.661A pdb=" N ILE D1716 " --> pdb=" O TYR D1712 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1734 removed outlier: 4.175A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU D1733 " --> pdb=" O SER D1729 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR D1734 " --> pdb=" O MET D1730 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 4.016A pdb=" N ALA D1744 " --> pdb=" O PRO D1740 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1825 Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 Processing helix chain 'D' and resid 1925 through 1930 removed outlier: 5.131A pdb=" N LYS D1930 " --> pdb=" O LEU D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1932 through 1984 removed outlier: 4.938A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 1997 removed outlier: 3.986A pdb=" N GLU D1990 " --> pdb=" O MET D1986 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D1996 " --> pdb=" O ALA D1992 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2012 removed outlier: 4.956A pdb=" N PHE D2012 " --> pdb=" O MET D2008 " (cutoff:3.500A) Processing helix chain 'D' and resid 2024 through 2043 Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.981A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 4.002A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2139 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.813A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2173 through 2188 removed outlier: 5.253A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D2178 " --> pdb=" O GLU D2174 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 Processing helix chain 'D' and resid 2195 through 2202 removed outlier: 3.827A pdb=" N GLY D2202 " --> pdb=" O MET D2198 " (cutoff:3.500A) Processing helix chain 'D' and resid 2203 through 2216 Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 3.910A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2254 Processing helix chain 'D' and resid 2255 through 2261 Processing helix chain 'D' and resid 2271 through 2282 removed outlier: 5.540A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) Processing helix chain 'D' and resid 2283 through 2290 removed outlier: 3.514A pdb=" N ALA D2287 " --> pdb=" O ASN D2283 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2306 removed outlier: 3.689A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY D2306 " --> pdb=" O LEU D2302 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 Processing helix chain 'D' and resid 2324 through 2340 Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.902A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 3.570A pdb=" N ALA D2421 " --> pdb=" O HIS D2417 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2439 through 2446 Processing helix chain 'D' and resid 2447 through 2462 removed outlier: 3.783A pdb=" N VAL D2461 " --> pdb=" O LEU D2457 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2463 through 2472 removed outlier: 3.607A pdb=" N LEU D2472 " --> pdb=" O GLY D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2495 through 2510 removed outlier: 3.989A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2525 removed outlier: 4.789A pdb=" N GLY D2525 " --> pdb=" O VAL D2521 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2537 Processing helix chain 'D' and resid 2544 through 2566 removed outlier: 4.619A pdb=" N LEU D2559 " --> pdb=" O CYS D2555 " (cutoff:3.500A) Proline residue: D2560 - end of helix Processing helix chain 'D' and resid 2575 through 2592 removed outlier: 3.653A pdb=" N ARG D2591 " --> pdb=" O TYR D2587 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY D2592 " --> pdb=" O ARG D2588 " (cutoff:3.500A) Processing helix chain 'D' and resid 2596 through 2614 removed outlier: 5.104A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2618 through 2633 Proline residue: D2631 - end of helix Processing helix chain 'D' and resid 2638 through 2652 Processing helix chain 'D' and resid 2669 through 2688 Processing helix chain 'D' and resid 2692 through 2707 Proline residue: D2701 - end of helix Processing helix chain 'D' and resid 2748 through 2774 Processing helix chain 'D' and resid 2793 through 2798 removed outlier: 4.819A pdb=" N SER D2798 " --> pdb=" O TYR D2794 " (cutoff:3.500A) Processing helix chain 'D' and resid 2799 through 2820 Proline residue: D2808 - end of helix Processing helix chain 'D' and resid 2861 through 2866 removed outlier: 4.039A pdb=" N VAL D2865 " --> pdb=" O ASP D2861 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR D2866 " --> pdb=" O LEU D2862 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2861 through 2866' Processing helix chain 'D' and resid 2868 through 2898 Processing helix chain 'D' and resid 2907 through 2912 removed outlier: 4.834A pdb=" N THR D2912 " --> pdb=" O TYR D2908 " (cutoff:3.500A) Processing helix chain 'D' and resid 2913 through 2934 removed outlier: 4.552A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) Processing helix chain 'D' and resid 2951 through 2979 removed outlier: 3.688A pdb=" N ALA D2979 " --> pdb=" O ALA D2975 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3014 removed outlier: 4.081A pdb=" N LEU D3002 " --> pdb=" O PHE D2998 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D3003 " --> pdb=" O ALA D2999 " (cutoff:3.500A) Proline residue: D3004 - end of helix Processing helix chain 'D' and resid 3034 through 3051 Processing helix chain 'D' and resid 3065 through 3073 Processing helix chain 'D' and resid 3089 through 3111 Processing helix chain 'D' and resid 3127 through 3150 Proline residue: D3138 - end of helix Processing helix chain 'D' and resid 3160 through 3175 Processing helix chain 'D' and resid 3187 through 3199 Processing helix chain 'D' and resid 3248 through 3257 Processing helix chain 'D' and resid 3267 through 3284 Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix Processing helix chain 'D' and resid 3309 through 3326 Processing helix chain 'D' and resid 3352 through 3379 Proline residue: D3360 - end of helix Processing helix chain 'D' and resid 3395 through 3424 Proline residue: D3410 - end of helix Processing helix chain 'D' and resid 3428 through 3449 removed outlier: 4.715A pdb=" N HIS D3449 " --> pdb=" O TRP D3445 " (cutoff:3.500A) Processing helix chain 'D' and resid 3450 through 3463 Processing helix chain 'D' and resid 3510 through 3525 Proline residue: D3519 - end of helix removed outlier: 5.076A pdb=" N CYS D3525 " --> pdb=" O GLY D3521 " (cutoff:3.500A) Processing helix chain 'D' and resid 3532 through 3543 Processing helix chain 'D' and resid 3545 through 3555 Processing helix chain 'D' and resid 3588 through 3611 Processing helix chain 'D' and resid 3625 through 3638 removed outlier: 4.452A pdb=" N PHE D3636 " --> pdb=" O VAL D3632 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG D3637 " --> pdb=" O VAL D3633 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3665 removed outlier: 4.018A pdb=" N LEU D3663 " --> pdb=" O ALA D3659 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR D3664 " --> pdb=" O ALA D3660 " (cutoff:3.500A) Processing helix chain 'D' and resid 3668 through 3679 removed outlier: 3.787A pdb=" N ARG D3672 " --> pdb=" O SER D3668 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 removed outlier: 3.536A pdb=" N THR D3711 " --> pdb=" O ARG D3707 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3735 Processing helix chain 'D' and resid 3752 through 3772 Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.113A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 removed outlier: 3.573A pdb=" N GLN D3813 " --> pdb=" O ASN D3809 " (cutoff:3.500A) Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 3.552A pdb=" N THR D3838 " --> pdb=" O ALA D3834 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3857 removed outlier: 3.502A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 Processing helix chain 'D' and resid 3896 through 3905 Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.634A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 5.065A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4007 removed outlier: 3.554A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4033 removed outlier: 5.503A pdb=" N GLY D4033 " --> pdb=" O SER D4029 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 Processing helix chain 'D' and resid 4053 through 4074 Processing helix chain 'D' and resid 4075 through 4082 removed outlier: 5.234A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.252A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4133 removed outlier: 4.535A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) Processing helix chain 'D' and resid 4134 through 4154 Processing helix chain 'D' and resid 4157 through 4168 Processing helix chain 'D' and resid 4169 through 4175 Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 4.410A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4225 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4324 through 4341 removed outlier: 4.076A pdb=" N ALA D4328 " --> pdb=" O ALA D4324 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4559 Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 3.976A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4640 through 4684 removed outlier: 4.225A pdb=" N TRP D4644 " --> pdb=" O GLU D4640 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS D4645 " --> pdb=" O PRO D4641 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix removed outlier: 3.760A pdb=" N PHE D4683 " --> pdb=" O ARG D4679 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP D4684 " --> pdb=" O LYS D4680 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4709 removed outlier: 4.338A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Proline residue: D4709 - end of helix Processing helix chain 'D' and resid 4719 through 4728 Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4745 through 4755 Processing helix chain 'D' and resid 4766 through 4771 Processing helix chain 'D' and resid 4772 through 4786 Processing helix chain 'D' and resid 4787 through 4806 Processing helix chain 'D' and resid 4807 through 4821 removed outlier: 5.134A pdb=" N ALA D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS D4821 " --> pdb=" O ALA D4817 " (cutoff:3.500A) Processing helix chain 'D' and resid 4822 through 4835 removed outlier: 3.603A pdb=" N THR D4831 " --> pdb=" O LEU D4827 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY D4834 " --> pdb=" O VAL D4830 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS D4835 " --> pdb=" O THR D4831 " (cutoff:3.500A) Processing helix chain 'D' and resid 4836 through 4858 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 5.284A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4897 through 4902 removed outlier: 3.535A pdb=" N ILE D4901 " --> pdb=" O ILE D4897 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4897 through 4902' Processing helix chain 'D' and resid 4909 through 4924 removed outlier: 3.556A pdb=" N ARG D4913 " --> pdb=" O TYR D4909 " (cutoff:3.500A) Processing helix chain 'D' and resid 4928 through 4957 Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 4.131A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 5.108A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 Processing helix chain 'D' and resid 4685 through 4690 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 56 through 67 removed outlier: 5.264A pdb=" N SER E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'K' and resid 38 through 43 removed outlier: 3.687A pdb=" N ARG K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 67 removed outlier: 5.374A pdb=" N SER K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.952A pdb=" N TYR K 82 " --> pdb=" O PRO K 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 66 removed outlier: 4.996A pdb=" N CYS J 65 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 84 Processing helix chain 'J' and resid 143 through 148 removed outlier: 3.643A pdb=" N TRP J 147 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TRP J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 143 through 148' Processing helix chain 'J' and resid 249 through 256 removed outlier: 4.502A pdb=" N ALA J 256 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 425 removed outlier: 3.789A pdb=" N GLY J 423 " --> pdb=" O ASP J 419 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS J 424 " --> pdb=" O SER J 420 " (cutoff:3.500A) Proline residue: J 425 - end of helix Processing helix chain 'J' and resid 437 through 453 removed outlier: 3.590A pdb=" N GLU J 453 " --> pdb=" O ILE J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 482 removed outlier: 4.114A pdb=" N GLY J 482 " --> pdb=" O PHE J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 497 removed outlier: 4.408A pdb=" N TYR J 497 " --> pdb=" O ARG J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 508 removed outlier: 4.229A pdb=" N TYR J 506 " --> pdb=" O HIS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 532 removed outlier: 4.796A pdb=" N LYS J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU J 517 " --> pdb=" O GLU J 513 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY J 532 " --> pdb=" O SER J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 545 removed outlier: 4.018A pdb=" N CYS J 537 " --> pdb=" O ASN J 533 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR J 542 " --> pdb=" O ALA J 538 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN J 543 " --> pdb=" O LEU J 539 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU J 544 " --> pdb=" O PHE J 540 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP J 545 " --> pdb=" O SER J 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 554 removed outlier: 4.167A pdb=" N ASP J 552 " --> pdb=" O VAL J 548 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG J 553 " --> pdb=" O SER J 549 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU J 554 " --> pdb=" O LYS J 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 571 removed outlier: 3.809A pdb=" N ILE J 560 " --> pdb=" O ALA J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 578 removed outlier: 4.226A pdb=" N ASN J 576 " --> pdb=" O PRO J 572 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE J 577 " --> pdb=" O GLU J 573 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE J 578 " --> pdb=" O VAL J 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 572 through 578' Processing helix chain 'J' and resid 579 through 593 removed outlier: 3.662A pdb=" N ILE J 583 " --> pdb=" O GLN J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 596 through 609 removed outlier: 3.764A pdb=" N LEU J 600 " --> pdb=" O ASN J 596 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS J 607 " --> pdb=" O LEU J 603 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL J 608 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N CYS J 609 " --> pdb=" O SER J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 629 removed outlier: 3.807A pdb=" N ASN J 624 " --> pdb=" O LEU J 620 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU J 625 " --> pdb=" O ILE J 621 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU J 626 " --> pdb=" O THR J 622 " (cutoff:3.500A) Proline residue: J 627 - end of helix Processing helix chain 'J' and resid 810 through 815 removed outlier: 4.695A pdb=" N ALA J 814 " --> pdb=" O PRO J 810 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL J 815 " --> pdb=" O CYS J 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 810 through 815' Processing helix chain 'J' and resid 847 through 853 Proline residue: J 853 - end of helix Processing helix chain 'J' and resid 865 through 888 removed outlier: 3.743A pdb=" N ARG J 869 " --> pdb=" O PRO J 865 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS J 873 " --> pdb=" O ARG J 869 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE J 887 " --> pdb=" O ALA J 883 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU J 888 " --> pdb=" O LEU J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 904 through 909 removed outlier: 3.748A pdb=" N VAL J 908 " --> pdb=" O HIS J 904 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN J 909 " --> pdb=" O PRO J 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 904 through 909' Processing helix chain 'J' and resid 914 through 936 Processing helix chain 'J' and resid 980 through 1004 Processing helix chain 'J' and resid 1028 through 1050 removed outlier: 3.661A pdb=" N GLY J1050 " --> pdb=" O LEU J1046 " (cutoff:3.500A) Processing helix chain 'J' and resid 1207 through 1212 removed outlier: 3.538A pdb=" N LEU J1211 " --> pdb=" O ASP J1207 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG J1212 " --> pdb=" O VAL J1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1207 through 1212' Processing helix chain 'J' and resid 1213 through 1218 removed outlier: 3.982A pdb=" N GLY J1218 " --> pdb=" O PHE J1214 " (cutoff:3.500A) Processing helix chain 'J' and resid 1444 through 1449 removed outlier: 3.987A pdb=" N VAL J1448 " --> pdb=" O GLU J1444 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TRP J1449 " --> pdb=" O PRO J1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1444 through 1449' Processing helix chain 'J' and resid 1465 through 1470 removed outlier: 5.749A pdb=" N ARG J1470 " --> pdb=" O LEU J1466 " (cutoff:3.500A) Processing helix chain 'J' and resid 1496 through 1501 Processing helix chain 'J' and resid 1574 through 1580 removed outlier: 3.854A pdb=" N ALA J1578 " --> pdb=" O PRO J1574 " (cutoff:3.500A) Processing helix chain 'J' and resid 1649 through 1657 removed outlier: 3.785A pdb=" N LEU J1653 " --> pdb=" O ASP J1649 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER J1654 " --> pdb=" O ILE J1650 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU J1655 " --> pdb=" O LEU J1651 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG J1656 " --> pdb=" O GLU J1652 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU J1657 " --> pdb=" O LEU J1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1649 through 1657' Processing helix chain 'J' and resid 1658 through 1675 Processing helix chain 'J' and resid 1678 through 1690 removed outlier: 3.741A pdb=" N SER J1687 " --> pdb=" O HIS J1683 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS J1688 " --> pdb=" O ALA J1684 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP J1690 " --> pdb=" O CYS J1686 " (cutoff:3.500A) Processing helix chain 'J' and resid 1691 through 1700 removed outlier: 3.718A pdb=" N GLU J1699 " --> pdb=" O LEU J1695 " (cutoff:3.500A) Processing helix chain 'J' and resid 1704 through 1719 Processing helix chain 'J' and resid 1720 through 1732 removed outlier: 4.328A pdb=" N SER J1732 " --> pdb=" O ARG J1728 " (cutoff:3.500A) Processing helix chain 'J' and resid 1739 through 1745 removed outlier: 3.798A pdb=" N ILE J1745 " --> pdb=" O GLU J1741 " (cutoff:3.500A) Processing helix chain 'J' and resid 1803 through 1825 Processing helix chain 'J' and resid 1833 through 1852 Proline residue: J1840 - end of helix removed outlier: 3.672A pdb=" N GLY J1852 " --> pdb=" O LEU J1848 " (cutoff:3.500A) Processing helix chain 'J' and resid 1855 through 1867 Processing helix chain 'J' and resid 1932 through 1981 removed outlier: 3.568A pdb=" N ASP J1967 " --> pdb=" O GLU J1963 " (cutoff:3.500A) Processing helix chain 'J' and resid 1989 through 2000 Processing helix chain 'J' and resid 2001 through 2012 removed outlier: 5.180A pdb=" N PHE J2012 " --> pdb=" O MET J2008 " (cutoff:3.500A) Processing helix chain 'J' and resid 2024 through 2043 removed outlier: 4.602A pdb=" N GLY J2043 " --> pdb=" O LEU J2039 " (cutoff:3.500A) Processing helix chain 'J' and resid 2093 through 2109 removed outlier: 3.650A pdb=" N ASP J2109 " --> pdb=" O TRP J2105 " (cutoff:3.500A) Processing helix chain 'J' and resid 2113 through 2130 removed outlier: 3.661A pdb=" N GLY J2130 " --> pdb=" O ARG J2126 " (cutoff:3.500A) Processing helix chain 'J' and resid 2131 through 2139 Proline residue: J2139 - end of helix Processing helix chain 'J' and resid 2145 through 2169 removed outlier: 4.139A pdb=" N VAL J2149 " --> pdb=" O SER J2145 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU J2150 " --> pdb=" O PRO J2146 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP J2151 " --> pdb=" O SER J2147 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J2167 " --> pdb=" O ARG J2163 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL J2168 " --> pdb=" O SER J2164 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN J2169 " --> pdb=" O LEU J2165 " (cutoff:3.500A) Processing helix chain 'J' and resid 2171 through 2189 removed outlier: 5.256A pdb=" N LYS J2189 " --> pdb=" O ILE J2185 " (cutoff:3.500A) Processing helix chain 'J' and resid 2190 through 2195 removed outlier: 3.726A pdb=" N HIS J2194 " --> pdb=" O VAL J2190 " (cutoff:3.500A) Proline residue: J2195 - end of helix No H-bonds generated for 'chain 'J' and resid 2190 through 2195' Processing helix chain 'J' and resid 2196 through 2202 Processing helix chain 'J' and resid 2203 through 2216 Processing helix chain 'J' and resid 2225 through 2244 removed outlier: 4.110A pdb=" N SER J2243 " --> pdb=" O PHE J2239 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG J2244 " --> pdb=" O CYS J2240 " (cutoff:3.500A) Processing helix chain 'J' and resid 2245 through 2254 removed outlier: 3.968A pdb=" N HIS J2253 " --> pdb=" O SER J2249 " (cutoff:3.500A) Processing helix chain 'J' and resid 2255 through 2261 Processing helix chain 'J' and resid 2271 through 2281 Processing helix chain 'J' and resid 2283 through 2290 Processing helix chain 'J' and resid 2291 through 2309 removed outlier: 4.138A pdb=" N LEU J2295 " --> pdb=" O GLN J2291 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER J2309 " --> pdb=" O CYS J2305 " (cutoff:3.500A) Processing helix chain 'J' and resid 2310 through 2317 removed outlier: 3.530A pdb=" N LEU J2314 " --> pdb=" O CYS J2310 " (cutoff:3.500A) Processing helix chain 'J' and resid 2324 through 2340 removed outlier: 3.641A pdb=" N GLY J2328 " --> pdb=" O ASN J2324 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG J2330 " --> pdb=" O CYS J2326 " (cutoff:3.500A) Processing helix chain 'J' and resid 2346 through 2361 removed outlier: 3.684A pdb=" N VAL J2352 " --> pdb=" O GLU J2348 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS J2360 " --> pdb=" O LEU J2356 " (cutoff:3.500A) Proline residue: J2361 - end of helix Processing helix chain 'J' and resid 2375 through 2390 Proline residue: J2390 - end of helix Processing helix chain 'J' and resid 2417 through 2446 Proline residue: J2438 - end of helix removed outlier: 8.987A pdb=" N HIS J2441 " --> pdb=" O ALA J2437 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU J2442 " --> pdb=" O PRO J2438 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY J2446 " --> pdb=" O LEU J2442 " (cutoff:3.500A) Processing helix chain 'J' and resid 2447 through 2462 removed outlier: 6.272A pdb=" N LEU J2451 " --> pdb=" O LYS J2447 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J2461 " --> pdb=" O LEU J2457 " (cutoff:3.500A) Proline residue: J2462 - end of helix Processing helix chain 'J' and resid 2463 through 2472 Processing helix chain 'J' and resid 2495 through 2509 removed outlier: 4.513A pdb=" N LYS J2499 " --> pdb=" O VAL J2495 " (cutoff:3.500A) Processing helix chain 'J' and resid 2514 through 2537 removed outlier: 4.932A pdb=" N GLY J2525 " --> pdb=" O VAL J2521 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE J2526 " --> pdb=" O LEU J2522 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU J2527 " --> pdb=" O ASP J2523 " (cutoff:3.500A) Proline residue: J2528 - end of helix Processing helix chain 'J' and resid 2544 through 2566 removed outlier: 4.368A pdb=" N LEU J2559 " --> pdb=" O CYS J2555 " (cutoff:3.500A) Proline residue: J2560 - end of helix Processing helix chain 'J' and resid 2575 through 2592 Processing helix chain 'J' and resid 2596 through 2614 Processing helix chain 'J' and resid 2615 through 2620 Processing helix chain 'J' and resid 2621 through 2630 removed outlier: 4.351A pdb=" N ASP J2629 " --> pdb=" O ARG J2625 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J2630 " --> pdb=" O LEU J2626 " (cutoff:3.500A) Processing helix chain 'J' and resid 2636 through 2652 Proline residue: J2640 - end of helix Processing helix chain 'J' and resid 2668 through 2689 Processing helix chain 'J' and resid 2692 through 2711 removed outlier: 4.280A pdb=" N MET J2700 " --> pdb=" O TYR J2696 " (cutoff:3.500A) Proline residue: J2701 - end of helix Proline residue: J2711 - end of helix Processing helix chain 'J' and resid 2748 through 2774 Processing helix chain 'J' and resid 2798 through 2820 Proline residue: J2808 - end of helix Processing helix chain 'J' and resid 2861 through 2866 removed outlier: 4.747A pdb=" N VAL J2865 " --> pdb=" O ASP J2861 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR J2866 " --> pdb=" O LEU J2862 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2861 through 2866' Processing helix chain 'J' and resid 2868 through 2898 Processing helix chain 'J' and resid 2914 through 2934 removed outlier: 4.043A pdb=" N ASP J2919 " --> pdb=" O GLU J2915 " (cutoff:3.500A) Processing helix chain 'J' and resid 2951 through 2979 Processing helix chain 'J' and resid 2991 through 3014 removed outlier: 3.611A pdb=" N LEU J3003 " --> pdb=" O ALA J2999 " (cutoff:3.500A) Proline residue: J3004 - end of helix Processing helix chain 'J' and resid 3033 through 3052 Processing helix chain 'J' and resid 3064 through 3073 Processing helix chain 'J' and resid 3089 through 3111 Processing helix chain 'J' and resid 3127 through 3150 Proline residue: J3138 - end of helix Processing helix chain 'J' and resid 3160 through 3175 Processing helix chain 'J' and resid 3187 through 3199 Processing helix chain 'J' and resid 3248 through 3257 Processing helix chain 'J' and resid 3269 through 3284 Proline residue: J3275 - end of helix Proline residue: J3282 - end of helix Processing helix chain 'J' and resid 3309 through 3326 Processing helix chain 'J' and resid 3337 through 3344 removed outlier: 3.549A pdb=" N GLN J3343 " --> pdb=" O ALA J3339 " (cutoff:3.500A) Proline residue: J3344 - end of helix Processing helix chain 'J' and resid 3350 through 3378 removed outlier: 3.770A pdb=" N LEU J3354 " --> pdb=" O ARG J3350 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE J3359 " --> pdb=" O HIS J3355 " (cutoff:3.500A) Proline residue: J3360 - end of helix Processing helix chain 'J' and resid 3395 through 3424 Proline residue: J3410 - end of helix Processing helix chain 'J' and resid 3428 through 3449 removed outlier: 3.663A pdb=" N SER J3448 " --> pdb=" O TYR J3444 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS J3449 " --> pdb=" O TRP J3445 " (cutoff:3.500A) Processing helix chain 'J' and resid 3450 through 3463 Processing helix chain 'J' and resid 3510 through 3524 Proline residue: J3519 - end of helix Processing helix chain 'J' and resid 3530 through 3543 Processing helix chain 'J' and resid 3546 through 3555 Processing helix chain 'J' and resid 3588 through 3611 Processing helix chain 'J' and resid 3625 through 3638 removed outlier: 3.502A pdb=" N ARG J3629 " --> pdb=" O SER J3625 " (cutoff:3.500A) Processing helix chain 'J' and resid 3640 through 3645 Proline residue: J3645 - end of helix Processing helix chain 'J' and resid 3646 through 3665 removed outlier: 4.945A pdb=" N LEU J3663 " --> pdb=" O ALA J3659 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR J3664 " --> pdb=" O ALA J3660 " (cutoff:3.500A) Processing helix chain 'J' and resid 3668 through 3679 removed outlier: 4.247A pdb=" N ARG J3672 " --> pdb=" O SER J3668 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS J3679 " --> pdb=" O ASP J3675 " (cutoff:3.500A) Processing helix chain 'J' and resid 3696 through 3711 removed outlier: 3.530A pdb=" N THR J3711 " --> pdb=" O ARG J3707 " (cutoff:3.500A) Processing helix chain 'J' and resid 3719 through 3735 removed outlier: 3.610A pdb=" N CYS J3733 " --> pdb=" O MET J3729 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J3734 " --> pdb=" O ALA J3730 " (cutoff:3.500A) Processing helix chain 'J' and resid 3752 through 3772 removed outlier: 3.850A pdb=" N LEU J3770 " --> pdb=" O GLN J3766 " (cutoff:3.500A) Processing helix chain 'J' and resid 3774 through 3787 removed outlier: 3.946A pdb=" N LYS J3787 " --> pdb=" O ILE J3783 " (cutoff:3.500A) Processing helix chain 'J' and resid 3791 through 3806 Processing helix chain 'J' and resid 3809 through 3824 removed outlier: 3.892A pdb=" N GLN J3813 " --> pdb=" O ASN J3809 " (cutoff:3.500A) Processing helix chain 'J' and resid 3827 through 3839 removed outlier: 3.583A pdb=" N CYS J3839 " --> pdb=" O LEU J3835 " (cutoff:3.500A) Processing helix chain 'J' and resid 3843 through 3856 removed outlier: 4.041A pdb=" N LEU J3856 " --> pdb=" O LYS J3852 " (cutoff:3.500A) Processing helix chain 'J' and resid 3877 through 3893 Processing helix chain 'J' and resid 3896 through 3906 Processing helix chain 'J' and resid 3914 through 3939 removed outlier: 4.542A pdb=" N CYS J3918 " --> pdb=" O ASN J3914 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY J3939 " --> pdb=" O TRP J3935 " (cutoff:3.500A) Processing helix chain 'J' and resid 3944 through 3970 Processing helix chain 'J' and resid 3973 through 3984 removed outlier: 3.898A pdb=" N SER J3983 " --> pdb=" O SER J3979 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG J3984 " --> pdb=" O LEU J3980 " (cutoff:3.500A) Processing helix chain 'J' and resid 3985 through 4007 removed outlier: 4.316A pdb=" N SER J4007 " --> pdb=" O LEU J4003 " (cutoff:3.500A) Processing helix chain 'J' and resid 4009 through 4033 removed outlier: 5.632A pdb=" N GLY J4033 " --> pdb=" O SER J4029 " (cutoff:3.500A) Processing helix chain 'J' and resid 4038 through 4052 Processing helix chain 'J' and resid 4053 through 4075 removed outlier: 5.057A pdb=" N GLU J4075 " --> pdb=" O ILE J4071 " (cutoff:3.500A) Processing helix chain 'J' and resid 4076 through 4082 removed outlier: 3.803A pdb=" N THR J4082 " --> pdb=" O GLN J4078 " (cutoff:3.500A) Processing helix chain 'J' and resid 4089 through 4100 removed outlier: 4.325A pdb=" N GLN J4100 " --> pdb=" O ALA J4096 " (cutoff:3.500A) Processing helix chain 'J' and resid 4104 through 4115 Processing helix chain 'J' and resid 4124 through 4137 removed outlier: 3.826A pdb=" N ARG J4131 " --> pdb=" O GLU J4127 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE J4132 " --> pdb=" O PHE J4128 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN J4133 " --> pdb=" O ALA J4129 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU J4134 " --> pdb=" O ASN J4130 " (cutoff:3.500A) Proline residue: J4135 - end of helix Processing helix chain 'J' and resid 4138 through 4155 Proline residue: J4155 - end of helix Processing helix chain 'J' and resid 4157 through 4168 removed outlier: 3.938A pdb=" N GLU J4168 " --> pdb=" O LEU J4164 " (cutoff:3.500A) Processing helix chain 'J' and resid 4169 through 4179 Proline residue: J4176 - end of helix removed outlier: 5.225A pdb=" N GLY J4179 " --> pdb=" O ARG J4175 " (cutoff:3.500A) Processing helix chain 'J' and resid 4198 through 4207 removed outlier: 3.637A pdb=" N GLU J4206 " --> pdb=" O ARG J4202 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N MET J4207 " --> pdb=" O ALA J4203 " (cutoff:3.500A) Processing helix chain 'J' and resid 4208 through 4224 Processing helix chain 'J' and resid 4226 through 4252 removed outlier: 4.353A pdb=" N MET J4231 " --> pdb=" O GLU J4227 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU J4232 " --> pdb=" O ALA J4228 " (cutoff:3.500A) Processing helix chain 'J' and resid 4323 through 4343 removed outlier: 4.099A pdb=" N ALA J4327 " --> pdb=" O THR J4323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA J4342 " --> pdb=" O VAL J4338 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY J4343 " --> pdb=" O VAL J4339 " (cutoff:3.500A) Processing helix chain 'J' and resid 4541 through 4559 removed outlier: 3.590A pdb=" N PHE J4559 " --> pdb=" O LEU J4555 " (cutoff:3.500A) Processing helix chain 'J' and resid 4560 through 4580 removed outlier: 3.987A pdb=" N PHE J4579 " --> pdb=" O PHE J4575 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR J4580 " --> pdb=" O ILE J4576 " (cutoff:3.500A) Processing helix chain 'J' and resid 4639 through 4683 removed outlier: 3.547A pdb=" N LYS J4665 " --> pdb=" O TYR J4661 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL J4666 " --> pdb=" O ASN J4662 " (cutoff:3.500A) Proline residue: J4667 - end of helix removed outlier: 3.812A pdb=" N PHE J4683 " --> pdb=" O ARG J4679 " (cutoff:3.500A) Processing helix chain 'J' and resid 4696 through 4707 removed outlier: 3.694A pdb=" N GLN J4700 " --> pdb=" O ASP J4696 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU J4704 " --> pdb=" O GLN J4700 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL J4705 " --> pdb=" O TRP J4701 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN J4707 " --> pdb=" O ARG J4703 " (cutoff:3.500A) Processing helix chain 'J' and resid 4719 through 4733 removed outlier: 5.191A pdb=" N ASP J4730 " --> pdb=" O ASP J4726 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE J4731 " --> pdb=" O LYS J4727 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE J4732 " --> pdb=" O HIS J4728 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY J4733 " --> pdb=" O GLY J4729 " (cutoff:3.500A) Processing helix chain 'J' and resid 4734 through 4742 Processing helix chain 'J' and resid 4745 through 4755 Processing helix chain 'J' and resid 4772 through 4787 removed outlier: 5.559A pdb=" N ASN J4787 " --> pdb=" O ILE J4783 " (cutoff:3.500A) Processing helix chain 'J' and resid 4788 through 4806 Processing helix chain 'J' and resid 4807 through 4820 removed outlier: 5.208A pdb=" N ALA J4811 " --> pdb=" O PHE J4807 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS J4812 " --> pdb=" O PHE J4808 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU J4813 " --> pdb=" O PHE J4809 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU J4814 " --> pdb=" O ALA J4810 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP J4815 " --> pdb=" O ALA J4811 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE J4816 " --> pdb=" O HIS J4812 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA J4817 " --> pdb=" O LEU J4813 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET J4818 " --> pdb=" O LEU J4814 " (cutoff:3.500A) Processing helix chain 'J' and resid 4821 through 4833 removed outlier: 3.743A pdb=" N THR J4831 " --> pdb=" O LEU J4827 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN J4833 " --> pdb=" O SER J4829 " (cutoff:3.500A) Processing helix chain 'J' and resid 4834 through 4858 Processing helix chain 'J' and resid 4859 through 4864 removed outlier: 4.956A pdb=" N TYR J4863 " --> pdb=" O PHE J4859 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN J4864 " --> pdb=" O ARG J4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4859 through 4864' Processing helix chain 'J' and resid 4878 through 4893 removed outlier: 3.729A pdb=" N LEU J4884 " --> pdb=" O MET J4880 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL J4891 " --> pdb=" O MET J4887 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG J4892 " --> pdb=" O TYR J4888 " (cutoff:3.500A) Processing helix chain 'J' and resid 4909 through 4924 Processing helix chain 'J' and resid 4928 through 4957 Processing helix chain 'J' and resid 4964 through 4970 removed outlier: 4.458A pdb=" N PHE J4968 " --> pdb=" O GLY J4964 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR J4970 " --> pdb=" O ASP J4966 " (cutoff:3.500A) Processing helix chain 'J' and resid 4973 through 4982 removed outlier: 3.679A pdb=" N GLU J4981 " --> pdb=" O THR J4977 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU J4982 " --> pdb=" O HIS J4978 " (cutoff:3.500A) Processing helix chain 'J' and resid 4984 through 4999 removed outlier: 5.046A pdb=" N ASP J4999 " --> pdb=" O LEU J4995 " (cutoff:3.500A) Processing helix chain 'J' and resid 5004 through 5017 Processing helix chain 'J' and resid 5027 through 5033 removed outlier: 3.823A pdb=" N TYR J5032 " --> pdb=" O PHE J5028 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 59 Proline residue: J 59 - end of helix No H-bonds generated for 'chain 'J' and resid 54 through 59' Processing helix chain 'J' and resid 308 through 313 removed outlier: 4.125A pdb=" N SER J 313 " --> pdb=" O HIS J 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 308 through 313' Processing helix chain 'J' and resid 4685 through 4690 removed outlier: 3.965A pdb=" N GLU J4690 " --> pdb=" O GLY J4685 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4685 through 4690' Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 29 through 41 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 67 through 93 removed outlier: 3.658A pdb=" N ARG L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS L 76 " --> pdb=" O MET L 72 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 114 Processing helix chain 'L' and resid 118 through 129 Processing helix chain 'L' and resid 138 through 148 Processing sheet with id= 1, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.679A pdb=" N LEU G 37 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N ALA G 39 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 13.997A pdb=" N VAL G 20 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'G' and resid 67 through 70 removed outlier: 5.205A pdb=" N LEU G 108 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU G 109 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET G 116 " --> pdb=" O HIS G 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'G' and resid 149 through 152 Processing sheet with id= 4, first strand: chain 'G' and resid 220 through 224 Processing sheet with id= 5, first strand: chain 'G' and resid 230 through 233 removed outlier: 5.022A pdb=" N VAL G 245 " --> pdb=" O ALA G 376 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'G' and resid 260 through 264 removed outlier: 4.853A pdb=" N ILE G 282 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG G 289 " --> pdb=" O HIS G 284 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 314 through 318 Processing sheet with id= 8, first strand: chain 'G' and resid 637 through 640 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'G' and resid 682 through 686 removed outlier: 4.122A pdb=" N ARG G 683 " --> pdb=" O SER G 782 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 754 through 758 removed outlier: 4.095A pdb=" N SER G 754 " --> pdb=" O ASP G 749 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP G 742 " --> pdb=" O VAL G 668 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS G 788 " --> pdb=" O ASP G 669 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 766 through 769 removed outlier: 3.519A pdb=" N SER G1485 " --> pdb=" O MET G1476 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 829 through 833 removed outlier: 4.013A pdb=" N LEU G1202 " --> pdb=" O PRO G 837 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN G1198 " --> pdb=" O GLY G 841 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL G1199 " --> pdb=" O VAL G1095 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY G1086 " --> pdb=" O LEU G1155 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU G1155 " --> pdb=" O GLY G1086 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP G1088 " --> pdb=" O ILE G1153 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA G1094 " --> pdb=" O ASP G1147 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP G1147 " --> pdb=" O ALA G1094 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G1161 " --> pdb=" O MET G1152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP G1154 " --> pdb=" O THR G1159 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 1135 through 1139 removed outlier: 5.129A pdb=" N GLY G1129 " --> pdb=" O PHE G1139 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN G1130 " --> pdb=" O ASN G1125 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N MET G1100 " --> pdb=" O GLY G1126 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG G1101 " --> pdb=" O SER G1193 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY G1103 " --> pdb=" O VAL G1191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G1077 " --> pdb=" O PRO G1190 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU G1194 " --> pdb=" O ARG G1073 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG G1073 " --> pdb=" O LEU G1194 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N VAL G1072 " --> pdb=" O SER G1241 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N SER G1241 " --> pdb=" O VAL G1072 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR G1236 " --> pdb=" O MET G1608 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER G1604 " --> pdb=" O LYS G1240 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 1243 through 1247 Processing sheet with id= 15, first strand: chain 'G' and resid 1267 through 1273 removed outlier: 3.816A pdb=" N ILE G1562 " --> pdb=" O LEU G1272 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL G1561 " --> pdb=" O PHE G1440 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE G1440 " --> pdb=" O VAL G1561 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY G1567 " --> pdb=" O TYR G1434 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR G1434 " --> pdb=" O GLY G1567 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR G1431 " --> pdb=" O LEU G1522 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G1514 " --> pdb=" O VAL G1439 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 1450 through 1453 Processing sheet with id= 17, first strand: chain 'G' and resid 2775 through 2778 Processing sheet with id= 18, first strand: chain 'G' and resid 2821 through 2825 removed outlier: 3.605A pdb=" N THR G2822 " --> pdb=" O THR G2938 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G2824 " --> pdb=" O ALA G2936 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 4177 through 4184 removed outlier: 5.337A pdb=" N TYR G4177 " --> pdb=" O ILE G4197 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY G4179 " --> pdb=" O PHE G4195 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE G4195 " --> pdb=" O GLY G4179 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 2 through 7 removed outlier: 3.859A pdb=" N GLU H 3 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA H 72 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL H 101 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP H 100 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU H 102 " --> pdb=" O HIS H 25 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.803A pdb=" N ARG B 71 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 98 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B 100 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 46 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 18 through 24 removed outlier: 5.763A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'A' and resid 34 through 39 removed outlier: 5.942A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.804A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 116 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'A' and resid 149 through 152 removed outlier: 3.608A pdb=" N ILE A 170 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 219 through 224 removed outlier: 5.781A pdb=" N VAL A 219 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 389 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 246 through 249 removed outlier: 3.924A pdb=" N GLY A 249 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 372 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'A' and resid 259 through 264 removed outlier: 8.414A pdb=" N LEU A 259 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 289 " --> pdb=" O HIS A 284 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.216A pdb=" N ARG A 683 " --> pdb=" O SER A 782 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS A 681 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'A' and resid 660 through 668 removed outlier: 7.632A pdb=" N GLY A 660 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'A' and resid 766 through 769 removed outlier: 3.582A pdb=" N GLU A 769 " --> pdb=" O THR A1473 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'A' and resid 789 through 792 removed outlier: 6.269A pdb=" N GLY A1625 " --> pdb=" O ALA A1620 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'A' and resid 829 through 832 removed outlier: 4.032A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY A1086 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A1094 " --> pdb=" O ASP A1147 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'A' and resid 1135 through 1138 removed outlier: 3.856A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP A1104 " --> pdb=" O TYR A1122 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG A1101 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A1193 " --> pdb=" O ARG A1101 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.683A pdb=" N GLN A1244 " --> pdb=" O MET A1601 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR A1546 " --> pdb=" O PHE A1297 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'A' and resid 1267 through 1273 removed outlier: 3.985A pdb=" N LEU A1270 " --> pdb=" O PHE A1564 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A1564 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'A' and resid 1517 through 1522 removed outlier: 3.619A pdb=" N LEU A1526 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A1525 " --> pdb=" O VAL A1542 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A1542 " --> pdb=" O GLY A1525 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'A' and resid 2780 through 2783 removed outlier: 7.421A pdb=" N ASN A2780 " --> pdb=" O PRO A2789 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A2782 " --> pdb=" O THR A2787 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'A' and resid 2821 through 2825 Processing sheet with id= 40, first strand: chain 'A' and resid 4177 through 4182 removed outlier: 5.129A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A4197 " --> pdb=" O TYR A4177 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A4179 " --> pdb=" O PHE A4195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A4195 " --> pdb=" O GLY A4179 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.354A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.649A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 148 through 152 Processing sheet with id= 44, first strand: chain 'D' and resid 220 through 224 Processing sheet with id= 45, first strand: chain 'D' and resid 229 through 233 removed outlier: 3.542A pdb=" N THR D 232 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL D 245 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'D' and resid 260 through 264 Processing sheet with id= 47, first strand: chain 'D' and resid 682 through 689 removed outlier: 5.959A pdb=" N LEU D 776 " --> pdb=" O THR D 689 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 755 through 759 removed outlier: 3.910A pdb=" N SER D 756 " --> pdb=" O CYS D 747 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 758 " --> pdb=" O SER D 745 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS D 746 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D1626 " --> pdb=" O PHE D 791 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'D' and resid 829 through 832 removed outlier: 4.596A pdb=" N TYR D 829 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 841 " --> pdb=" O GLN D1198 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D1093 " --> pdb=" O HIS D1201 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU D1091 " --> pdb=" O ASN D1203 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLY D1086 " --> pdb=" O LEU D1155 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU D1155 " --> pdb=" O GLY D1086 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS D1151 " --> pdb=" O PHE D1090 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE D1092 " --> pdb=" O VAL D1149 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'D' and resid 1073 through 1076 removed outlier: 3.874A pdb=" N CYS D1192 " --> pdb=" O PHE D1075 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D1101 " --> pdb=" O SER D1193 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR D1122 " --> pdb=" O TRP D1104 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'D' and resid 1237 through 1241 Processing sheet with id= 52, first strand: chain 'D' and resid 1256 through 1263 No H-bonds generated for sheet with id= 52 Processing sheet with id= 53, first strand: chain 'D' and resid 1286 through 1291 Processing sheet with id= 54, first strand: chain 'D' and resid 1294 through 1297 removed outlier: 3.504A pdb=" N VAL D1295 " --> pdb=" O LEU D1548 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR D1546 " --> pdb=" O PHE D1297 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 1431 through 1436 removed outlier: 7.911A pdb=" N THR D1431 " --> pdb=" O LEU D1522 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D1522 " --> pdb=" O THR D1431 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLY D1517 " --> pdb=" O THR D1530 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D1530 " --> pdb=" O GLY D1517 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP D1521 " --> pdb=" O LEU D1526 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D1526 " --> pdb=" O ASP D1521 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY D1525 " --> pdb=" O VAL D1542 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 1473 through 1476 removed outlier: 3.729A pdb=" N LEU D1487 " --> pdb=" O VAL D1474 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET D1476 " --> pdb=" O SER D1485 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 2780 through 2783 removed outlier: 7.008A pdb=" N ASN D2780 " --> pdb=" O PRO D2789 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D2787 " --> pdb=" O ASP D2782 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 2821 through 2825 Processing sheet with id= 59, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 5.049A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D4179 " --> pdb=" O PHE D4195 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D4195 " --> pdb=" O GLY D4179 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE D4193 " --> pdb=" O ILE D4181 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D4183 " --> pdb=" O GLU D4191 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D4191 " --> pdb=" O ILE D4183 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.878A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'E' and resid 45 through 50 removed outlier: 3.609A pdb=" N ILE E 50 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN E 20 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.466A pdb=" N GLU K 3 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU K 5 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG K 71 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA K 72 " --> pdb=" O VAL K 101 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL K 101 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR K 27 " --> pdb=" O ASP K 100 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS K 25 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 47 through 51 removed outlier: 7.340A pdb=" N LEU J 33 " --> pdb=" O ALA J 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS J 24 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU J 22 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N ALA J 39 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 13.457A pdb=" N VAL J 20 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 19 " --> pdb=" O ILE J 205 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN J 203 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN J 23 " --> pdb=" O ASN J 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN J 201 " --> pdb=" O GLN J 23 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 67 through 70 removed outlier: 5.026A pdb=" N LEU J 108 " --> pdb=" O GLU J 70 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'J' and resid 149 through 152 Processing sheet with id= 66, first strand: chain 'J' and resid 178 through 182 Processing sheet with id= 67, first strand: chain 'J' and resid 220 through 224 Processing sheet with id= 68, first strand: chain 'J' and resid 230 through 234 removed outlier: 3.602A pdb=" N THR J 232 " --> pdb=" O TYR J 246 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR J 246 " --> pdb=" O THR J 232 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU J 244 " --> pdb=" O SER J 234 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'J' and resid 260 through 265 removed outlier: 5.979A pdb=" N ILE J 282 " --> pdb=" O LEU J 291 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 289 " --> pdb=" O HIS J 284 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'J' and resid 637 through 640 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'J' and resid 681 through 684 removed outlier: 6.864A pdb=" N HIS J 681 " --> pdb=" O SER J 784 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG J 683 " --> pdb=" O SER J 782 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'J' and resid 714 through 717 removed outlier: 5.283A pdb=" N HIS J 720 " --> pdb=" O ASP J 717 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU J 719 " --> pdb=" O VAL J 730 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG J 728 " --> pdb=" O LEU J 721 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'J' and resid 754 through 759 removed outlier: 4.201A pdb=" N SER J 754 " --> pdb=" O ASP J 749 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP J 742 " --> pdb=" O VAL J 668 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU J 665 " --> pdb=" O LEU J 792 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS J 788 " --> pdb=" O ASP J 669 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'J' and resid 766 through 769 Processing sheet with id= 75, first strand: chain 'J' and resid 829 through 832 removed outlier: 4.362A pdb=" N TYR J 829 " --> pdb=" O VAL J 840 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU J1202 " --> pdb=" O PRO J 837 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN J1198 " --> pdb=" O GLY J 841 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL J1199 " --> pdb=" O VAL J1095 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU J1091 " --> pdb=" O ASN J1203 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY J1086 " --> pdb=" O LEU J1155 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'J' and resid 1005 through 1008 removed outlier: 3.858A pdb=" N SER J1008 " --> pdb=" O ASN J1018 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'J' and resid 1099 through 1104 removed outlier: 6.263A pdb=" N GLU J1099 " --> pdb=" O GLY J1195 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG J1101 " --> pdb=" O SER J1193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU J1194 " --> pdb=" O ARG J1073 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG J1073 " --> pdb=" O LEU J1194 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N VAL J1072 " --> pdb=" O SER J1241 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER J1241 " --> pdb=" O VAL J1072 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE J1074 " --> pdb=" O SER J1239 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER J1239 " --> pdb=" O ILE J1074 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'J' and resid 1122 through 1126 removed outlier: 3.570A pdb=" N VAL J1123 " --> pdb=" O TRP J1132 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY J1129 " --> pdb=" O PHE J1139 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'J' and resid 1243 through 1247 removed outlier: 3.963A pdb=" N GLN J1244 " --> pdb=" O MET J1601 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET J1601 " --> pdb=" O GLN J1244 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR J1546 " --> pdb=" O PHE J1297 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'J' and resid 1255 through 1262 removed outlier: 3.528A pdb=" N LEU J1566 " --> pdb=" O PRO J1268 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU J1272 " --> pdb=" O ILE J1562 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE J1562 " --> pdb=" O LEU J1272 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG J1438 " --> pdb=" O GLN J1563 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY J1567 " --> pdb=" O TYR J1434 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR J1434 " --> pdb=" O GLY J1567 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU J1514 " --> pdb=" O VAL J1439 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU J1526 " --> pdb=" O ASP J1521 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY J1525 " --> pdb=" O VAL J1542 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE J1540 " --> pdb=" O MET J1527 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'J' and resid 1733 through 1737 removed outlier: 3.508A pdb=" N TYR J2142 " --> pdb=" O TYR J1734 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL J1736 " --> pdb=" O TYR J2142 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'J' and resid 2821 through 2825 removed outlier: 3.535A pdb=" N THR J2822 " --> pdb=" O THR J2938 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR J2938 " --> pdb=" O THR J2822 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU J2824 " --> pdb=" O ALA J2936 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'J' and resid 4180 through 4184 7270 hydrogen bonds defined for protein. 21735 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: 72.23 Time building geometry restraints manager: 35.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 25710 1.33 - 1.46: 23129 1.46 - 1.58: 58513 1.58 - 1.70: 23 1.70 - 1.82: 713 Bond restraints: 108088 Sorted by residual: bond pdb=" N VAL J4154 " pdb=" CA VAL J4154 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" N ILE A 377 " pdb=" CA ILE A 377 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.08e-02 8.57e+03 1.06e+01 bond pdb=" CA LEU G4017 " pdb=" C LEU G4017 " ideal model delta sigma weight residual 1.522 1.566 -0.044 1.39e-02 5.18e+03 1.00e+01 bond pdb=" N GLY K 86 " pdb=" CA GLY K 86 " ideal model delta sigma weight residual 1.444 1.474 -0.031 1.02e-02 9.61e+03 8.98e+00 bond pdb=" N VAL D4036 " pdb=" CA VAL D4036 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.67e+00 ... (remaining 108083 not shown) Histogram of bond angle deviations from ideal: 94.98 - 103.96: 1534 103.96 - 112.95: 60011 112.95 - 121.93: 64847 121.93 - 130.91: 21673 130.91 - 139.90: 479 Bond angle restraints: 148544 Sorted by residual: angle pdb=" N HIS D2125 " pdb=" CA HIS D2125 " pdb=" C HIS D2125 " ideal model delta sigma weight residual 111.36 102.47 8.89 1.09e+00 8.42e-01 6.65e+01 angle pdb=" N VAL A4045 " pdb=" CA VAL A4045 " pdb=" C VAL A4045 " ideal model delta sigma weight residual 110.42 102.71 7.71 9.60e-01 1.09e+00 6.45e+01 angle pdb=" N LEU A 494 " pdb=" CA LEU A 494 " pdb=" C LEU A 494 " ideal model delta sigma weight residual 111.28 103.12 8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" N ASP D3671 " pdb=" CA ASP D3671 " pdb=" C ASP D3671 " ideal model delta sigma weight residual 111.36 103.35 8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" N ASP G4018 " pdb=" CA ASP G4018 " pdb=" C ASP G4018 " ideal model delta sigma weight residual 111.14 103.53 7.61 1.08e+00 8.57e-01 4.96e+01 ... (remaining 148539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 57241 18.17 - 36.35: 4113 36.35 - 54.52: 1086 54.52 - 72.70: 119 72.70 - 90.87: 54 Dihedral angle restraints: 62613 sinusoidal: 14712 harmonic: 47901 Sorted by residual: dihedral pdb=" CB BCYS M 10 " pdb=" SG BCYS M 10 " pdb=" SG BCYS M 21 " pdb=" CB BCYS M 21 " ideal model delta sinusoidal sigma weight residual -86.00 -167.03 81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB ACYS M 10 " pdb=" SG ACYS M 10 " pdb=" SG ACYS M 21 " pdb=" CB ACYS M 21 " ideal model delta sinusoidal sigma weight residual -86.00 -163.75 77.75 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB BCYS M 16 " pdb=" SG BCYS M 16 " pdb=" SG BCYS M 32 " pdb=" CB BCYS M 32 " ideal model delta sinusoidal sigma weight residual 93.00 141.60 -48.60 1 1.00e+01 1.00e-02 3.25e+01 ... (remaining 62610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 16849 0.076 - 0.152: 1299 0.152 - 0.228: 95 0.228 - 0.304: 6 0.304 - 0.380: 4 Chirality restraints: 18253 Sorted by residual: chirality pdb=" CA VAL A4045 " pdb=" N VAL A4045 " pdb=" C VAL A4045 " pdb=" CB VAL A4045 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CG LEU G4017 " pdb=" CB LEU G4017 " pdb=" CD1 LEU G4017 " pdb=" CD2 LEU G4017 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA VAL A3989 " pdb=" N VAL A3989 " pdb=" C VAL A3989 " pdb=" CB VAL A3989 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 18250 not shown) Planarity restraints: 19495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS J2194 " -0.081 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO J2195 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO J2195 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO J2195 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2171 " 0.076 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A2172 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A2172 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A2172 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A4237 " 0.030 2.00e-02 2.50e+03 3.26e-02 1.85e+01 pdb=" CG PHE A4237 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE A4237 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A4237 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A4237 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A4237 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A4237 " 0.005 2.00e-02 2.50e+03 ... (remaining 19492 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6551 2.74 - 3.28: 109377 3.28 - 3.82: 189449 3.82 - 4.36: 179301 4.36 - 4.90: 324274 Nonbonded interactions: 808952 Sorted by model distance: nonbonded pdb=" O ASN D3963 " pdb=" OG1 THR D3966 " model vdw 2.200 2.440 nonbonded pdb=" NE2 GLN A 475 " pdb=" O ARG A 531 " model vdw 2.210 2.520 nonbonded pdb=" OD1AASN M 27 " pdb=" N AALA M 28 " model vdw 2.218 2.520 nonbonded pdb=" OD1 ASN J 576 " pdb=" NE2 GLN J2169 " model vdw 2.223 2.520 nonbonded pdb=" O ILE G3674 " pdb=" OG SER G3678 " model vdw 2.225 2.440 ... (remaining 808947 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 12 through 13 or (resid 14 through 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 or (resid 25 through 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 or (resid 42 and ( \ name N or name CA or name C or name O or name CB )) or resid 43 or (resid 44 and \ (name N or name CA or name C or name O or name CB )) or resid 45 through 46 or \ (resid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 o \ r (resid 49 through 66 and (name N or name CA or name C or name O or name CB )) \ or resid 67 or (resid 68 through 73 and (name N or name CA or name C or name O o \ r name CB )) or resid 74 or (resid 75 through 84 and (name N or name CA or name \ C or name O or name CB )) or resid 97 or (resid 98 through 99 and (name N or nam \ e CA or name C or name O or name CB )) or resid 100 or (resid 101 and (name N or \ name CA or name C or name O or name CB )) or resid 102 through 106 or (resid 10 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 108 through \ 109 or (resid 110 through 118 and (name N or name CA or name C or name O or name \ CB )) or resid 119 or (resid 120 through 125 and (name N or name CA or name C o \ r name O or name CB )) or resid 130 through 133 or (resid 134 and (name N or nam \ e CA or name C or name O or name CB )) or resid 135 through 136 or (resid 137 th \ rough 142 and (name N or name CA or name C or name O or name CB )) or (resid 143 \ through 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 47 through 149 or (resid 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 through 162 or (resid 163 through 165 and (name N or name CA \ or name C or name O or name CB )) or resid 166 through 170 or (resid 171 and (na \ me N or name CA or name C or name O or name CB )) or resid 172 through 174 or (r \ esid 175 through 178 and (name N or name CA or name C or name O or name CB )) or \ resid 179 through 193 or (resid 194 and (name N or name CA or name C or name O \ or name CB )) or resid 195 through 201 or (resid 202 through 203 and (name N or \ name CA or name C or name O or name CB )) or resid 204 through 205 or (resid 213 \ through 215 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 16 through 217 or (resid 218 through 224 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 229 through 235 and (name N or name CA or name C or \ name O or name CB )) or (resid 242 through 248 and (name N or name CA or name C \ or name O or name CB )) or resid 249 through 252 or (resid 254 through 257 and ( \ name N or name CA or name C or name O or name CB )) or resid 258 through 263 or \ (resid 264 through 268 and (name N or name CA or name C or name O or name CB )) \ or resid 269 through 277 or (resid 278 and (name N or name CA or name C or name \ O or name CB )) or resid 279 or (resid 280 through 287 and (name N or name CA or \ name C or name O or name CB )) or (resid 288 through 291 and (name N or name CA \ or name C or name O or name CB )) or (resid 300 through 318 and (name N or name \ CA or name C or name O or name CB )) or (resid 346 through 353 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 354 through 360 and (name N o \ r name CA or name C or name O or name CB )) or (resid 372 through 381 and (name \ N or name CA or name C or name O or name CB )) or (resid 382 through 404 and (na \ me N or name CA or name C or name O or name CB )) or resid 405 through 418 or (r \ esid 419 and (name N or name CA or name C or name O or name CB )) or resid 420 t \ hrough 426 or resid 436 through 437 or (resid 438 through 449 and (name N or nam \ e CA or name C or name O or name CB )) or resid 450 through 455 or resid 465 thr \ ough 467 or (resid 468 through 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470 or (resid 471 through 475 and (name N or name CA or nam \ e C or name O or name CB )) or resid 476 or (resid 477 through 481 and (name N o \ r name CA or name C or name O or name CB )) or resid 482 or (resid 483 through 4 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 485 or (res \ id 486 through 488 and (name N or name CA or name C or name O or name CB )) or r \ esid 489 or (resid 490 through 495 and (name N or name CA or name C or name O or \ name CB )) or resid 496 through 498 or (resid 499 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 509 through 514 and (name N or name CA or \ name C or name O or name CB )) or resid 515 through 517 or (resid 518 through 51 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 520 or (resi \ d 521 through 522 and (name N or name CA or name C or name O or name CB )) or re \ sid 523 through 525 or (resid 526 through 527 and (name N or name CA or name C o \ r name O or name CB )) or resid 528 through 529 or (resid 530 through 531 and (n \ ame N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 th \ rough 545 and (name N or name CA or name C or name O or name CB )) or resid 546 \ or (resid 547 through 557 and (name N or name CA or name C or name O or name CB \ )) or resid 558 through 559 or (resid 560 and (name N or name CA or name C or na \ me O or name CB )) or resid 561 through 563 or (resid 564 and (name N or name CA \ or name C or name O or name CB )) or resid 565 through 573 or (resid 574 throug \ h 575 and (name N or name CA or name C or name O or name CB )) or resid 576 or ( \ resid 577 through 581 and (name N or name CA or name C or name O or name CB )) o \ r resid 582 through 585 or (resid 586 through 587 and (name N or name CA or name \ C or name O or name CB )) or resid 588 through 589 or (resid 590 through 592 an \ d (name N or name CA or name C or name O or name CB )) or resid 593 through 594 \ or (resid 595 and (name N or name CA or name C or name O or name CB )) or resid \ 596 through 598 or (resid 599 and (name N or name CA or name C or name O or name \ CB )) or resid 600 through 602 or (resid 603 and (name N or name CA or name C o \ r name O or name CB )) or resid 604 through 608 or (resid 609 through 610 and (n \ ame N or name CA or name C or name O or name CB )) or resid 611 through 617 or ( \ resid 618 through 620 and (name N or name CA or name C or name O or name CB )) o \ r resid 621 or (resid 622 through 626 and (name N or name CA or name C or name O \ or name CB )) or resid 627 through 631 or (resid 632 through 635 and (name N or \ name CA or name C or name O or name CB )) or resid 636 or (resid 637 through 63 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 641 or (resid 642 through 645 and (name N or name CA or name C or name O or name \ CB )) or resid 646 or (resid 647 through 649 and (name N or name CA or name C o \ r name O or name CB )) or resid 650 through 656 or (resid 657 through 658 and (n \ ame N or name CA or name C or name O or name CB )) or resid 659 through 667 or ( \ resid 668 through 684 and (name N or name CA or name C or name O or name CB )) o \ r resid 685 through 690 or resid 702 through 706 or (resid 707 and (name N or na \ me CA or name C or name O or name CB )) or (resid 708 through 711 and (name N or \ name CA or name C or name O or name CB )) or resid 712 or (resid 713 and (name \ N or name CA or name C or name O or name CB )) or resid 714 through 715 or (resi \ d 716 through 717 and (name N or name CA or name C or name O or name CB )) or (r \ esid 718 through 723 and (name N or name CA or name C or name O or name CB )) or \ resid 724 or (resid 725 through 729 and (name N or name CA or name C or name O \ or name CB )) or (resid 735 through 739 and (name N or name CA or name C or name \ O or name CB )) or resid 740 through 744 or (resid 745 through 760 and (name N \ or name CA or name C or name O or name CB )) or resid 761 or (resid 762 through \ 765 and (name N or name CA or name C or name O or name CB )) or resid 766 or (re \ sid 767 through 774 and (name N or name CA or name C or name O or name CB )) or \ resid 775 or (resid 776 through 777 and (name N or name CA or name C or name O o \ r name CB )) or resid 778 through 779 or (resid 780 through 781 and (name N or n \ ame CA or name C or name O or name CB )) or resid 782 or (resid 783 through 785 \ and (name N or name CA or name C or name O or name CB )) or resid 786 or (resid \ 787 through 793 and (name N or name CA or name C or name O or name CB )) or (res \ id 794 through 797 and (name N or name CA or name C or name O or name CB )) or ( \ resid 798 through 806 and (name N or name CA or name C or name O or name CB )) o \ r resid 807 or (resid 808 through 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 816 or (resid 817 through 828 and (name N or \ name CA or name C or name O or name CB )) or resid 829 through 834 or (resid 83 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 838 or (resi \ d 839 through 840 and (name N or name CA or name C or name O or name CB )) or re \ sid 841 or (resid 848 through 853 and (name N or name CA or name C or name O or \ name CB )) or (resid 865 through 925 and (name N or name CA or name C or name O \ or name CB )) or resid 926 through 936 or (resid 985 through 991 and (name N or \ name CA or name C or name O or name CB )) or (resid 992 through 1003 and (name N \ or name CA or name C or name O or name CB )) or resid 1004 or (resid 1005 throu \ gh 1047 and (name N or name CA or name C or name O or name CB )) or resid 1048 o \ r (resid 1049 and (name N or name CA or name C or name O or name CB )) or resid \ 1050 or (resid 1071 through 1080 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1081 through 1082 or (resid 1083 through 1085 and (name N or \ name CA or name C or name O or name CB )) or (resid 1086 through 1097 and (name \ N or name CA or name C or name O or name CB )) or resid 1098 through 1105 or (re \ sid 1106 and (name N or name CA or name C or name O or name CB )) or resid 1107 \ through 1108 or (resid 1109 through 1110 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1111 through 1112 or (resid 1113 through 1115 and (na \ me N or name CA or name C or name O or name CB )) or (resid 1116 through 1125 an \ d (name N or name CA or name C or name O or name CB )) or resid 1126 or (resid 1 \ 127 through 1128 and (name N or name CA or name C or name O or name CB )) or res \ id 1129 or (resid 1130 through 1134 and (name N or name CA or name C or name O o \ r name CB )) or resid 1135 or (resid 1136 through 1137 and (name N or name CA or \ name C or name O or name CB )) or resid 1138 or (resid 1139 and (name N or name \ CA or name C or name O or name CB )) or resid 1140 or (resid 1141 and (name N o \ r name CA or name C or name O or name CB )) or resid 1142 through 1144 or (resid \ 1145 and (name N or name CA or name C or name O or name CB )) or resid 1146 thr \ ough 1148 or (resid 1149 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1150 or (resid 1151 through 1165 and (name N or name CA or name C or \ name O or name CB )) or (resid 1166 through 1173 and (name N or name CA or name \ C or name O or name CB )) or (resid 1174 through 1184 and (name N or name CA or \ name C or name O or name CB )) or (resid 1185 through 1194 and (name N or name C \ A or name C or name O or name CB )) or resid 1195 or (resid 1196 and (name N or \ name CA or name C or name O or name CB )) or (resid 1197 through 1199 and (name \ N or name CA or name C or name O or name CB )) or resid 1200 through 1201 or (re \ sid 1202 through 1204 and (name N or name CA or name C or name O or name CB )) o \ r resid 1205 or (resid 1206 through 1217 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1218 through 1225 or (resid 1226 through 1228 and (na \ me N or name CA or name C or 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4983 through 4988 or (resid 4989 and (name N or name CA \ or name C or name O or name CB )) or resid 4990 through 4998 or (resid 4999 thro \ ugh 5000 and (name N or name CA or name C or name O or name CB )) or resid 5001 \ through 5036 or resid 5101 through 5104)) selection = (chain 'G' and ((resid 12 and (name N or name CA or name C or name O or name CB \ )) or resid 13 through 15 or (resid 16 through 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 26 or (resid 32 through 40 and (n \ ame N or name CA or name C or name O or name CB )) or resid 41 or (resid 42 and \ (name N or name CA or name C or name O or name CB )) or resid 43 or (resid 44 an \ d (name N or name CA or name C or name O or name CB )) or resid 45 through 46 or \ (resid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 \ or (resid 49 through 66 and (name N or name CA or name C or name O or name CB )) \ or resid 67 or (resid 68 through 73 and (name N or name CA or 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2280 or (resid 2281 through 2285 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2286 through 2289 or ( \ resid 2290 through 2294 and (name N or name CA or name C or name O or name CB )) \ or resid 2295 through 2298 or (resid 2299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 2300 through 2311 or (resid 2312 through 2316 and ( \ name N or name CA or name C or name O or name CB )) or resid 2317 or (resid 2318 \ and (name N or name CA or name C or name O or name CB )) or resid 2319 through \ 2340 or (resid 2341 through 2342 and (name N or name CA or name C or name O or n \ ame CB )) or resid 2343 through 2348 or (resid 2349 through 2351 and (name N or \ name CA or name C or name O or name CB )) or resid 2352 or (resid 2353 and (name \ N or name CA or name C or name O or name CB )) or resid 2354 through 2357 or (r \ esid 2358 through 2360 and (name N or name CA or name C or name O or name CB )) \ or resid 2361 through 2376 or (resid 2377 through 2389 and (name N or name CA or \ name C or name O or name CB )) or resid 2390 or resid 2415 through 2431 or (res \ id 2432 through 2433 and (name N or name CA or name C or name O or name CB )) or \ resid 2434 through 2442 or (resid 2443 through 2445 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 2446 through 2455 and (name N or name CA \ or name C or name O or name CB )) or resid 2456 through 2462 or (resid 2463 thr \ ough 2467 and (name N or name CA or name C or name O or name CB )) or resid 2468 \ through 2476 or (resid 2477 and (name N or name CA or name C or name O or name \ CB )) or (resid 2487 through 2495 and (name N or name CA or name C or name O or \ name CB )) or resid 2496 through 2500 or (resid 2501 through 2502 and (name N or \ name CA or name C or name O or name CB )) or resid 2503 through 2507 or (resid \ 2508 through 2509 and (name N or name CA or name C or name O or name CB )) or re \ sid 2510 through 2516 or (resid 2517 through 2524 and (name N or name CA or name \ C or name O or name CB )) or resid 2525 or (resid 2526 through 2527 and (name N \ or name CA or name C or name O or name CB )) or resid 2528 through 2529 or (res \ id 2530 through 2550 and (name N or name CA or name C or name O or name CB )) or \ resid 2551 through 2562 or (resid 2563 through 2566 and (name N or name CA or n \ ame C or name O or name CB )) or resid 2567 or (resid 2568 and (name N or name C \ A or name C or name O or name CB )) or resid 2569 through 2578 or (resid 2579 th \ rough 2586 and (name N or name CA or name C or name O or name CB )) or resid 258 \ 7 through 2588 or (resid 2589 through 2591 and (name N or name CA or name C or n \ ame O or name CB )) or resid 2592 through 2601 or (resid 2602 through 2650 and ( \ name N or name CA or name C or name O or name CB )) or (resid 2669 through 2680 \ and (name N or name CA or name C or name O or name CB )) or (resid 2681 through \ 2705 and (name N or name CA or name C or name O or name CB )) or resid 2749 thro \ ugh 2939 or resid 2955 through 2974 or resid 2994 through 3013 or resid 3035 thr \ ough 3049 or resid 3064 through 3108 or resid 3127 through 3149 or resid 3160 th \ rough 3175 or resid 3188 through 3197 or resid 3275 through 3326 or resid 3340 o \ r resid 3342 or (resid 3344 and (name N or name CA or name C or name O or name C \ B )) or resid 3354 through 3378 or resid 3396 through 3461 or resid 3511 through \ 3523 or resid 3530 through 3551 or (resid 3590 through 3638 and (name N or name \ CA or name C or name O or name CB )) or resid 3639 through 3640 or (resid 3641 \ and (name N or name CA or name C or name O or name CB )) or resid 3642 through 3 \ 647 or (resid 3648 through 3649 and (name N or name CA or name C or name O or na \ me CB )) or resid 3650 or (resid 3651 through 3652 and (name N or name CA or nam \ e C or name O or name CB )) or resid 3653 or (resid 3654 through 3655 and (name \ N or name CA or name C or name O or name CB )) or resid 3656 through 3662 or (re \ sid 3663 through 3668 and (name N or name CA or name C or name O or name CB )) o \ r resid 3669 through 3681 or (resid 3693 through 3694 and (name N or name CA or \ name C or name O or name CB )) or resid 3695 or (resid 3696 and (name N or name \ CA or name C or name O or name CB )) or resid 3697 through 3706 or (resid 3707 a \ nd (name N or name CA or name C or name O or name CB )) or resid 3708 through 37 \ 09 or (resid 3710 and (name N or name CA or name C or name O or name CB )) or re \ sid 3711 through 3715 or (resid 3716 through 3719 and (name N or name CA or name \ C or name O or name CB )) or resid 3720 through 3726 or (resid 3727 and (name N \ or name CA or name C or name O or name CB )) or resid 3728 through 3730 or (res \ id 3731 and (name N or name CA or name C or name O or name CB )) or resid 3732 t \ hrough 3734 or (resid 3735 through 3751 and (name N or name CA or name C or name \ O or name CB )) or resid 3752 through 3757 or (resid 3758 through 3760 and (nam \ e N or name CA or name C or name O or name CB )) or resid 3761 or (resid 3762 an \ d (name N or name CA or name C or name O or name CB )) or resid 3763 through 378 \ 0 or (resid 3781 and (name N or name CA or name C or name O or name CB )) or res \ id 3782 through 3785 or (resid 3786 through 3787 and (name N or name CA or name \ C or name O or name CB )) or resid 3788 through 3829 or (resid 3830 and (name N \ or name CA or name C or name O or name CB )) or resid 3831 through 3844 or (resi \ d 3845 through 3846 and (name N or name CA or name C or name O or name CB )) or \ resid 3847 through 3863 or resid 3872 through 3874 or (resid 3875 through 3879 a \ nd (name N or name CA or name C or name O or name CB )) or resid 3880 through 39 \ 06 or (resid 3907 and (name N or name CA or name C or name O or name CB )) or (r \ esid 3908 through 3913 and (name N or name CA or name C or name O or name CB )) \ or resid 3914 through 3941 or (resid 3942 and (name N or name CA or name C or na \ me O or name CB )) or resid 3943 through 3976 or (resid 3977 and (name N or name \ CA or name C or name O or name CB )) or resid 3978 through 4020 or (resid 4021 \ and (name N or name CA or name C or name O or name CB )) or resid 4022 through 4 \ 058 or (resid 4059 through 4060 and (name N or name CA or name C or name O or na \ me CB )) or resid 4061 through 4076 or (resid 4077 through 4079 and (name N or n \ ame CA or name C or name O or name CB )) or resid 4080 or (resid 4081 through 40 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 4084 throug \ h 4096 or (resid 4097 through 4104 and (name N or name CA or name C or name O or \ name CB )) or resid 4105 through 4107 or (resid 4108 through 4109 and (name N o \ r name CA or name C or name O or name CB )) or resid 4110 or (resid 4111 through \ 4112 and (name N or name CA or name C or name O or name CB )) or resid 4113 thr \ ough 4114 or (resid 4115 through 4134 and (name N or name CA or name C or name O \ or name CB )) or resid 4135 through 4136 or (resid 4137 through 4139 and (name \ N or name CA or name C or name O or name CB )) or resid 4140 through 4186 or (re \ sid 4187 through 4192 and (name N or name CA or name C or name O or name CB )) o \ r resid 4193 through 4195 or (resid 4196 and (name N or name CA or name C or nam \ e O or name CB )) or resid 4197 through 4203 or (resid 4204 and (name N or name \ CA or name C or name O or name CB )) or resid 4205 through 4238 or (resid 4239 t \ hrough 4240 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 41 through 4245 or (resid 4246 and (name N or name CA or name C or name O or nam \ e CB )) or resid 4247 through 4250 or (resid 4251 and (name N or name CA or name \ C or name O or name CB )) or resid 4252 through 4341 or resid 4541 through 4547 \ or (resid 4548 and (name N or name CA or name C or name O or name CB )) or resi \ d 4549 through 4631 or (resid 4632 through 4636 and (name N or name CA or name C \ or name O or name CB )) or resid 4637 or (resid 4638 and (name N or name CA or \ name C or name O or name CB )) or resid 4639 through 4664 or (resid 4665 and (na \ me N or name CA or name C or name O or name CB )) or resid 4666 through 4675 or \ (resid 4676 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 77 through 4687 or (resid 4688 through 4691 and (name N or name CA or name C or \ name O or name CB )) or resid 4692 through 4717 or (resid 4718 and (name N or na \ me CA or name C or name O or name CB )) or resid 4719 through 4720 or (resid 472 \ 1 through 4723 and (name N or name CA or name C or name O or name CB )) or resid \ 4724 or (resid 4725 through 4728 and (name N or name CA or name C or name O or \ name CB )) or (resid 4729 through 4732 and (name N or name CA or name C or name \ O or name CB )) or resid 4733 or (resid 4734 through 4739 and (name N or name CA \ or name C or name O or name CB )) or resid 4740 or (resid 4741 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 4742 through 4772 and (name N \ or name CA or name C or name O or name CB )) or resid 4773 through 4899 or (res \ id 4900 and (name N or name CA or name C or name O or name CB )) or resid 4901 o \ r (resid 4902 through 4903 and (name N or name CA or name C or name O or name CB \ )) or resid 4904 through 4937 or (resid 4938 through 4939 and (name N or name C \ A or name C or name O or name CB )) or resid 4940 through 4951 or (resid 4952 th \ rough 4953 and (name N or name CA or name C or name O or name CB )) or resid 495 \ 4 or (resid 4955 and (name N or name CA or name C or name O or name CB )) or res \ id 4956 through 4998 or (resid 4999 through 5000 and (name N or name CA or name \ C or name O or name CB )) or resid 5001 through 5011 or (resid 5012 and (name N \ or name CA or name C or name O or name CB )) or resid 5013 through 5035 or (resi \ d 5036 and (name N or name CA or name C or name O or name CB )) or resid 5101 th \ rough 5104)) } ncs_group { reference = (chain 'B' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 33 or (resid 34 throug \ h 35 and (name N or name CA or name C or name O or name CB )) or resid 36 or (re \ sid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 thro \ ugh 39 or (resid 40 through 42 and (name N or name CA or name C or name O or nam \ e CB )) or resid 43 or (resid 44 and (name N or name CA or name C or name O or n \ ame CB )) or resid 45 through 47 or (resid 48 through 49 and (name N or name CA \ or name C or name O or name CB )) or resid 50 through 55 or (resid 56 through 57 \ and (name N or name CA or name C or name O or name CB )) or resid 58 through 64 \ or (resid 65 through 66 and (name N or name CA or name C or name O or name CB ) \ ) or resid 67 through 70 or (resid 71 through 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 89 or (resid 90 and (name N or nam \ e CA or name C or name O or name CB )) or resid 91 through 93 or (resid 94 throu \ gh 95 and (name N or name CA or name C or name O or name CB )) or resid 96 or (r \ esid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 thr \ ough 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) o \ r resid 101 or (resid 102 through 106 and (name N or name CA or name C or name O \ or name CB )))) selection = (chain 'E' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 106)) selection = (chain 'H' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 28 or (resid 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 33 or (re \ sid 34 through 35 and (name N or name CA or name C or name O or name CB )) or re \ sid 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or \ resid 38 through 39 or (resid 40 through 42 and (name N or name CA or name C or \ name O or name CB )) or resid 43 through 46 or (resid 47 through 49 and (name N \ or name CA or name C or name O or name CB )) or resid 50 through 53 or (resid 54 \ and (name N or name CA or name C or name O or name CB )) or resid 55 or (resid \ 56 through 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 through 64 or (resid 65 through 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 70 or (resid 71 through 73 and (name N or nam \ e CA or name C or name O or name CB )) or resid 74 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 93 or (r \ esid 94 through 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O or \ name CB )) or resid 101 or (resid 102 through 106 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 28 or (resid 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 33 or (re \ sid 34 through 35 and (name N or name CA or name C or name O or name CB )) or re \ sid 36 through 39 or (resid 40 through 42 and (name N or name CA or name C or na \ me O or name CB )) or resid 43 or (resid 44 and (name N or name CA or name C or \ name O or name CB )) or resid 45 through 46 or (resid 47 through 49 and (name N \ or name CA or name C or name O or name CB )) or resid 50 through 53 or (resid 54 \ and (name N or name CA or name C or name O or name CB )) or resid 55 or (resid \ 56 through 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 through 64 or (resid 65 through 66 and (name N or name CA or name C or name O \ or name CB )) or resid 67 through 70 or (resid 71 through 73 and (name N or nam \ e CA or name C or name O or name CB )) or resid 74 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 93 or (r \ esid 94 through 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O or \ name CB )) or resid 101 or (resid 102 through 106 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'C' and ((resid 1 through 23 and (name N or name CA or name C or name O o \ r name CB )) or (resid 24 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 or (resid 71 through 96 and (name N or na \ me CA or name C or name O or name CB )) or resid 97 through 148)) selection = (chain 'F' and ((resid 1 through 33 and (name N or name CA or name C or name O o \ r name CB )) or resid 34 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 89 or (resid 90 through 96 and (na \ me N or name CA or name C or name O or name CB )) or (resid 97 through 113 and ( \ name N or name CA or name C or name O or name CB )) or resid 114 through 148)) selection = (chain 'I' and ((resid 1 through 23 and (name N or name CA or name C or name O o \ r name CB )) or resid 24 through 56 or resid 63 through 72 or (resid 73 through \ 96 and (name N or name CA or name C or name O or name CB )) or resid 97 through \ 148)) selection = (chain 'L' and (resid 1 through 56 or resid 63 through 68 or (resid 69 and (name \ N or name CA or name C or name O or name CB )) or resid 70 through 72 or (resid \ 73 through 96 and (name N or name CA or name C or name O or name CB )) or resid \ 97 through 148)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 20.770 Check model and map are aligned: 1.130 Set scattering table: 0.680 Process input model: 331.900 Find NCS groups from input model: 11.480 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 372.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 0.102 108088 Z= 0.193 Angle : 0.566 12.951 148544 Z= 0.328 Chirality : 0.040 0.380 18253 Planarity : 0.003 0.120 19495 Dihedral : 14.445 90.871 31370 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.48 % Favored : 98.51 % Rotamer: Outliers : 1.25 % Allowed : 30.36 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.77 (0.07), residues: 16088 helix: 3.07 (0.05), residues: 9135 sheet: 0.00 (0.15), residues: 1298 loop : 0.23 (0.08), residues: 5655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP J2105 HIS 0.012 0.001 HIS G3771 PHE 0.074 0.001 PHE A4237 TYR 0.049 0.001 TYR G2331 ARG 0.006 0.000 ARG G4679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1197 time to evaluate : 8.809 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 483 MET cc_start: 0.7943 (ppp) cc_final: 0.7115 (ppp) REVERT: C 1 MET cc_start: 0.6772 (ppp) cc_final: 0.6395 (tmm) REVERT: D 4023 MET cc_start: 0.8432 (ttp) cc_final: 0.8154 (ttp) REVERT: D 4146 LEU cc_start: 0.8610 (tp) cc_final: 0.8396 (tp) REVERT: J 3967 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6451 (tp30) outliers start: 87 outliers final: 46 residues processed: 1250 average time/residue: 0.7946 time to fit residues: 1830.0801 Evaluate side-chains 1196 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1150 time to evaluate : 7.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 725 HIS Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2197 LEU Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3965 LEU Chi-restraints excluded: chain G residue 4631 PHE Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2142 TYR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3995 VAL Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 5019 TRP Chi-restraints excluded: chain D residue 3677 LEU Chi-restraints excluded: chain D residue 3732 SER Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3995 VAL Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4128 PHE Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4238 CYS Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4859 PHE Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3727 ASP Chi-restraints excluded: chain J residue 3728 ILE Chi-restraints excluded: chain J residue 4023 MET Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4146 LEU Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4886 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 1389 optimal weight: 0.8980 chunk 1246 optimal weight: 9.9990 chunk 691 optimal weight: 20.0000 chunk 425 optimal weight: 6.9990 chunk 841 optimal weight: 2.9990 chunk 666 optimal weight: 30.0000 chunk 1289 optimal weight: 10.0000 chunk 498 optimal weight: 8.9990 chunk 784 optimal weight: 3.9990 chunk 959 optimal weight: 7.9990 chunk 1493 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 ASN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1598 GLN G1688 HIS G1702 HIS ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3813 GLN G3851 ASN G3895 HIS ** G4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G4034 ASN ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4204 GLN G4574 ASN A 105 HIS A 218 HIS A 495 ASN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1640 HIS ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1837 GLN A4043 GLN A4223 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS D2194 HIS ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3900 GLN D4020 GLN D4037 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4707 ASN D4857 ASN ** J 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 634 GLN ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1696 HIS J2041 HIS J2107 GLN ** J2169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J3851 ASN J4142 ASN ** J4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J4832 HIS J4886 HIS J5003 HIS K 31 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 108088 Z= 0.389 Angle : 0.606 11.413 148544 Z= 0.317 Chirality : 0.040 0.302 18253 Planarity : 0.004 0.077 19495 Dihedral : 4.584 85.060 17257 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.63 % Allowed : 26.77 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.07), residues: 16088 helix: 2.84 (0.05), residues: 9230 sheet: -0.47 (0.15), residues: 1357 loop : 0.14 (0.08), residues: 5501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP G1104 HIS 0.011 0.002 HIS J1719 PHE 0.045 0.002 PHE A4237 TYR 0.025 0.002 TYR D3968 ARG 0.008 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 392 poor density : 1084 time to evaluate : 8.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 601 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: G 1760 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6870 (t-170) REVERT: G 2203 MET cc_start: 0.8097 (mpp) cc_final: 0.7798 (mtm) REVERT: G 2664 PHE cc_start: 0.8077 (m-80) cc_final: 0.7291 (t80) REVERT: G 3817 LEU cc_start: 0.9051 (tp) cc_final: 0.8717 (tt) REVERT: G 4679 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7582 (mpp80) REVERT: G 4980 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8332 (tp) REVERT: A 483 MET cc_start: 0.7835 (ppp) cc_final: 0.7453 (ppp) REVERT: A 494 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9078 (mm) REVERT: A 1522 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5056 (mm) REVERT: A 3723 MET cc_start: 0.8149 (mmp) cc_final: 0.7450 (mmt) REVERT: A 4064 MET cc_start: 0.7759 (pmm) cc_final: 0.7234 (pmm) REVERT: B 4 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 1 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6814 (tmm) REVERT: D 148 TRP cc_start: 0.6246 (m100) cc_final: 0.5796 (m100) REVERT: D 2290 LEU cc_start: 0.8981 (tp) cc_final: 0.8644 (mt) REVERT: D 3928 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7544 (mm-30) REVERT: D 4023 MET cc_start: 0.8052 (ttp) cc_final: 0.7769 (ttp) REVERT: D 4028 LEU cc_start: 0.8974 (mt) cc_final: 0.8758 (mt) REVERT: D 4047 MET cc_start: 0.8193 (ttp) cc_final: 0.7989 (ttm) REVERT: D 4580 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.6986 (t80) REVERT: J 478 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6815 (t80) REVERT: J 601 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7936 (t0) REVERT: J 1665 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8507 (m-70) REVERT: J 1844 LEU cc_start: 0.9097 (tp) cc_final: 0.8843 (tt) REVERT: J 2198 MET cc_start: 0.8334 (tpp) cc_final: 0.8063 (tpp) REVERT: J 2228 MET cc_start: 0.8369 (ppp) cc_final: 0.8098 (tmm) REVERT: J 2312 MET cc_start: 0.7108 (ppp) cc_final: 0.6005 (ptt) REVERT: J 2546 MET cc_start: 0.7377 (tpp) cc_final: 0.6853 (tpp) REVERT: J 3725 TYR cc_start: 0.8918 (m-80) cc_final: 0.8473 (m-80) REVERT: J 3979 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8907 (t) REVERT: J 4027 LEU cc_start: 0.8589 (mt) cc_final: 0.8186 (mm) REVERT: J 4103 PHE cc_start: 0.2117 (OUTLIER) cc_final: 0.1458 (m-80) outliers start: 392 outliers final: 229 residues processed: 1385 average time/residue: 0.7845 time to fit residues: 2006.3333 Evaluate side-chains 1263 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1020 time to evaluate : 8.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 521 LEU Chi-restraints excluded: chain G residue 600 LEU Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 640 TYR Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 789 VAL Chi-restraints excluded: chain G residue 849 THR Chi-restraints excluded: chain G residue 1123 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1184 ILE Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1191 VAL Chi-restraints excluded: chain G residue 1235 THR Chi-restraints excluded: chain G residue 1430 THR Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1495 VAL Chi-restraints excluded: chain G residue 1552 VAL Chi-restraints excluded: chain G residue 1553 PHE Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1640 HIS Chi-restraints excluded: chain G residue 1654 SER Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1760 HIS Chi-restraints excluded: chain G residue 1848 LEU Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2368 LEU Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2451 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2587 TYR Chi-restraints excluded: chain G residue 3667 HIS Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3708 THR Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3771 HIS Chi-restraints excluded: chain G residue 3794 VAL Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3965 LEU Chi-restraints excluded: chain G residue 3973 CYS Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4150 LEU Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4646 LEU Chi-restraints excluded: chain G residue 4658 ILE Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4679 ARG Chi-restraints excluded: chain G residue 4830 VAL Chi-restraints excluded: chain G residue 4852 THR Chi-restraints excluded: chain G residue 4914 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 5010 VAL Chi-restraints excluded: chain G residue 5027 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1640 HIS Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1842 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3783 ILE Chi-restraints excluded: chain A residue 3796 SER Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3892 CYS Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4016 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4569 LEU Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4897 ILE Chi-restraints excluded: chain A residue 4915 VAL Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain A residue 5010 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 607 CYS Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2339 VAL Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 3916 ILE Chi-restraints excluded: chain D residue 3930 ILE Chi-restraints excluded: chain D residue 3995 VAL Chi-restraints excluded: chain D residue 4111 LEU Chi-restraints excluded: chain D residue 4193 ILE Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4652 LEU Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4815 ASP Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4915 VAL Chi-restraints excluded: chain D residue 4979 THR Chi-restraints excluded: chain D residue 4985 LEU Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 601 ASP Chi-restraints excluded: chain J residue 605 SER Chi-restraints excluded: chain J residue 625 LEU Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 642 THR Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 1177 THR Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1430 THR Chi-restraints excluded: chain J residue 1431 THR Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1520 VAL Chi-restraints excluded: chain J residue 1603 VAL Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1665 HIS Chi-restraints excluded: chain J residue 1716 ILE Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1771 LEU Chi-restraints excluded: chain J residue 1830 VAL Chi-restraints excluded: chain J residue 1850 VAL Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2010 LEU Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2152 THR Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2207 VAL Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 3673 MET Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3721 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 3990 VAL Chi-restraints excluded: chain J residue 3993 LEU Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4146 LEU Chi-restraints excluded: chain J residue 4147 LEU Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4576 ILE Chi-restraints excluded: chain J residue 4801 LEU Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4950 VAL Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 830 optimal weight: 7.9990 chunk 463 optimal weight: 2.9990 chunk 1243 optimal weight: 8.9990 chunk 1017 optimal weight: 3.9990 chunk 412 optimal weight: 3.9990 chunk 1496 optimal weight: 7.9990 chunk 1616 optimal weight: 4.9990 chunk 1332 optimal weight: 2.9990 chunk 1484 optimal weight: 4.9990 chunk 510 optimal weight: 0.0870 chunk 1200 optimal weight: 0.6980 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1688 HIS ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3851 ASN ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4204 GLN ** G4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 639 ASN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4987 ASN D 405 HIS D2029 GLN D4162 ASN D4707 ASN ** J 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J3851 ASN J4201 ASN J4886 HIS K 43 ASN K 87 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 108088 Z= 0.228 Angle : 0.487 11.700 148544 Z= 0.248 Chirality : 0.037 0.174 18253 Planarity : 0.003 0.072 19495 Dihedral : 4.209 84.309 17211 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.46 % Allowed : 28.36 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.70 (0.07), residues: 16088 helix: 3.08 (0.05), residues: 9203 sheet: -0.54 (0.15), residues: 1354 loop : 0.18 (0.08), residues: 5531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G1104 HIS 0.018 0.001 HIS A1640 PHE 0.024 0.001 PHE D2683 TYR 0.022 0.001 TYR D3968 ARG 0.005 0.000 ARG D3984 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1092 time to evaluate : 8.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 194 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.6359 (p) REVERT: G 1494 MET cc_start: 0.7524 (mpp) cc_final: 0.6518 (mpp) REVERT: G 1760 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6925 (t70) REVERT: G 2198 MET cc_start: 0.8739 (mmm) cc_final: 0.7591 (mmm) REVERT: G 2384 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7936 (tp) REVERT: G 2664 PHE cc_start: 0.8031 (m-80) cc_final: 0.7264 (t80) REVERT: G 3817 LEU cc_start: 0.8985 (tp) cc_final: 0.8697 (tp) REVERT: G 3967 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6811 (mm-30) REVERT: G 4195 PHE cc_start: 0.8649 (p90) cc_final: 0.8412 (p90) REVERT: G 4652 LEU cc_start: 0.9433 (tp) cc_final: 0.9222 (tt) REVERT: G 4956 THR cc_start: 0.8918 (t) cc_final: 0.8702 (t) REVERT: G 4980 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8336 (tp) REVERT: H 25 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8139 (m-70) REVERT: A 483 MET cc_start: 0.7732 (ppp) cc_final: 0.7408 (ppp) REVERT: A 1522 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5138 (mm) REVERT: A 1865 MET cc_start: 0.8049 (ppp) cc_final: 0.7389 (ppp) REVERT: A 2097 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7629 (tp) REVERT: A 3721 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 3723 MET cc_start: 0.8201 (mmp) cc_final: 0.7718 (mmt) REVERT: A 4064 MET cc_start: 0.7797 (pmm) cc_final: 0.7330 (pmm) REVERT: A 4562 LEU cc_start: 0.8834 (tp) cc_final: 0.8600 (tp) REVERT: C 1 MET cc_start: 0.7007 (ppp) cc_final: 0.6768 (tmm) REVERT: D 2290 LEU cc_start: 0.9025 (tp) cc_final: 0.8689 (mt) REVERT: D 2696 TYR cc_start: 0.4971 (m-80) cc_final: 0.4162 (m-80) REVERT: D 4023 MET cc_start: 0.7997 (ttp) cc_final: 0.7785 (ttp) REVERT: D 4580 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.6571 (t80) REVERT: J 478 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6729 (t80) REVERT: J 1500 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6244 (p90) REVERT: J 1844 LEU cc_start: 0.9038 (tp) cc_final: 0.8794 (tp) REVERT: J 2107 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: J 2170 MET cc_start: 0.7455 (tpt) cc_final: 0.7070 (mmm) REVERT: J 2198 MET cc_start: 0.8290 (tpp) cc_final: 0.8037 (tpp) REVERT: J 2228 MET cc_start: 0.8286 (ppp) cc_final: 0.7901 (tmm) REVERT: J 2312 MET cc_start: 0.7190 (ppp) cc_final: 0.5991 (ptt) REVERT: J 3725 TYR cc_start: 0.8882 (m-80) cc_final: 0.8575 (m-80) REVERT: J 3979 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8828 (t) REVERT: J 4103 PHE cc_start: 0.2237 (OUTLIER) cc_final: 0.1711 (m-80) outliers start: 310 outliers final: 194 residues processed: 1327 average time/residue: 0.7622 time to fit residues: 1869.1088 Evaluate side-chains 1247 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1039 time to evaluate : 8.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 521 LEU Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 600 LEU Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 789 VAL Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1760 HIS Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2368 LEU Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 3018 LEU Chi-restraints excluded: chain G residue 3667 HIS Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3708 THR Chi-restraints excluded: chain G residue 3721 LEU Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3771 HIS Chi-restraints excluded: chain G residue 3910 THR Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4051 SER Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4169 SER Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4241 THR Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4658 ILE Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4830 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain G residue 5027 CYS Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4577 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4897 ILE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 2190 VAL Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 3844 LEU Chi-restraints excluded: chain D residue 3916 ILE Chi-restraints excluded: chain D residue 4111 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4652 LEU Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4915 VAL Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 563 VAL Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 588 SER Chi-restraints excluded: chain J residue 625 LEU Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1123 VAL Chi-restraints excluded: chain J residue 1177 THR Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1432 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1520 VAL Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1771 LEU Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 2010 LEU Chi-restraints excluded: chain J residue 2107 GLN Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2152 THR Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2186 MET Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2233 CYS Chi-restraints excluded: chain J residue 2257 LEU Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3673 MET Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3721 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 3990 VAL Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4147 LEU Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4686 LEU Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4850 LEU Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4937 ILE Chi-restraints excluded: chain J residue 4950 VAL Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 1478 optimal weight: 5.9990 chunk 1125 optimal weight: 20.0000 chunk 776 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 714 optimal weight: 0.9990 chunk 1004 optimal weight: 4.9990 chunk 1501 optimal weight: 20.0000 chunk 1590 optimal weight: 4.9990 chunk 784 optimal weight: 4.9990 chunk 1423 optimal weight: 10.0000 chunk 428 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3851 ASN ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G4857 ASN A 218 HIS A 495 ASN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2194 HIS A4223 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS D4020 GLN D4707 ASN J 576 ASN ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J2169 GLN J3781 GLN J3851 ASN K 31 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 108088 Z= 0.193 Angle : 0.471 10.381 148544 Z= 0.238 Chirality : 0.037 0.243 18253 Planarity : 0.003 0.067 19495 Dihedral : 4.065 83.438 17199 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.06 % Allowed : 28.01 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.07), residues: 16088 helix: 3.14 (0.05), residues: 9197 sheet: -0.55 (0.14), residues: 1366 loop : 0.18 (0.09), residues: 5525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G1104 HIS 0.010 0.001 HIS A1640 PHE 0.040 0.001 PHE A3996 TYR 0.024 0.001 TYR A 640 ARG 0.006 0.000 ARG D3984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1084 time to evaluate : 8.522 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: G 194 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.6382 (p) REVERT: G 601 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: G 1494 MET cc_start: 0.7328 (mpp) cc_final: 0.6511 (mpp) REVERT: G 1760 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6921 (t-170) REVERT: G 1851 MET cc_start: 0.8831 (mmm) cc_final: 0.8392 (mmm) REVERT: G 2198 MET cc_start: 0.8720 (mmm) cc_final: 0.7835 (mmm) REVERT: G 2384 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7934 (tp) REVERT: G 2664 PHE cc_start: 0.8106 (m-80) cc_final: 0.7342 (t80) REVERT: G 3723 MET cc_start: 0.8961 (mmt) cc_final: 0.8636 (mmt) REVERT: G 3817 LEU cc_start: 0.8966 (tp) cc_final: 0.8675 (tp) REVERT: G 3967 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6820 (mm-30) REVERT: G 4064 MET cc_start: 0.8061 (ptp) cc_final: 0.7823 (ptp) REVERT: G 4195 PHE cc_start: 0.8670 (p90) cc_final: 0.8429 (p90) REVERT: G 4956 THR cc_start: 0.8841 (t) cc_final: 0.8594 (t) REVERT: G 4980 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8330 (tp) REVERT: G 4992 LEU cc_start: 0.8929 (tp) cc_final: 0.8628 (tt) REVERT: H 25 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8126 (m-70) REVERT: A 483 MET cc_start: 0.7816 (ppp) cc_final: 0.7530 (ppp) REVERT: A 1865 MET cc_start: 0.8077 (ppp) cc_final: 0.7530 (ppp) REVERT: A 2097 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 2153 MET cc_start: 0.8314 (mmp) cc_final: 0.8113 (mmp) REVERT: A 3721 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 3723 MET cc_start: 0.8058 (mmp) cc_final: 0.7555 (mmt) REVERT: A 3890 LEU cc_start: 0.8735 (mp) cc_final: 0.8468 (mp) REVERT: A 4064 MET cc_start: 0.7996 (pmm) cc_final: 0.7664 (pmm) REVERT: A 4562 LEU cc_start: 0.8793 (tp) cc_final: 0.8411 (tp) REVERT: A 4639 MET cc_start: 0.7888 (mmt) cc_final: 0.7603 (mmt) REVERT: D 2290 LEU cc_start: 0.9079 (tp) cc_final: 0.8814 (mt) REVERT: D 2696 TYR cc_start: 0.4916 (m-80) cc_final: 0.4390 (m-80) REVERT: D 3927 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 4023 MET cc_start: 0.7769 (ttp) cc_final: 0.7519 (ttp) REVERT: D 4580 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.6506 (t80) REVERT: J 478 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6780 (t80) REVERT: J 1500 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6315 (p90) REVERT: J 1659 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8815 (mm) REVERT: J 2170 MET cc_start: 0.7412 (tpt) cc_final: 0.7099 (mmm) REVERT: J 2198 MET cc_start: 0.8298 (tpp) cc_final: 0.8010 (tpp) REVERT: J 2228 MET cc_start: 0.8282 (ppp) cc_final: 0.7965 (tmm) REVERT: J 2312 MET cc_start: 0.7221 (ppp) cc_final: 0.5990 (ptt) REVERT: J 2546 MET cc_start: 0.7517 (tpp) cc_final: 0.6804 (tpp) REVERT: J 3652 MET cc_start: 0.8154 (mtm) cc_final: 0.7723 (mtm) REVERT: J 3979 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8816 (t) REVERT: J 4103 PHE cc_start: 0.2277 (OUTLIER) cc_final: 0.1671 (m-80) REVERT: J 4577 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8629 (tt) outliers start: 351 outliers final: 238 residues processed: 1354 average time/residue: 0.7871 time to fit residues: 1971.4236 Evaluate side-chains 1299 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1046 time to evaluate : 8.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 446 GLN Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 789 VAL Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1520 VAL Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1654 SER Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1760 HIS Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 1955 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2368 LEU Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 3667 HIS Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3708 THR Chi-restraints excluded: chain G residue 3721 LEU Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3910 THR Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4051 SER Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4241 THR Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4658 ILE Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain G residue 5027 CYS Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1716 ILE Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3905 THR Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3969 ILE Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4915 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1695 LEU Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1717 SER Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 3844 LEU Chi-restraints excluded: chain D residue 3916 ILE Chi-restraints excluded: chain D residue 4111 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4652 LEU Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4915 VAL Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 563 VAL Chi-restraints excluded: chain J residue 588 SER Chi-restraints excluded: chain J residue 605 SER Chi-restraints excluded: chain J residue 625 LEU Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1123 VAL Chi-restraints excluded: chain J residue 1177 THR Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1430 THR Chi-restraints excluded: chain J residue 1432 THR Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1520 VAL Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1659 LEU Chi-restraints excluded: chain J residue 1715 LEU Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1771 LEU Chi-restraints excluded: chain J residue 1830 VAL Chi-restraints excluded: chain J residue 1846 SER Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2010 LEU Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2152 THR Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2169 GLN Chi-restraints excluded: chain J residue 2186 MET Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3673 MET Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3721 LEU Chi-restraints excluded: chain J residue 3732 SER Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3951 PHE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4577 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4686 LEU Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4850 LEU Chi-restraints excluded: chain J residue 4876 CYS Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4937 ILE Chi-restraints excluded: chain J residue 4950 VAL Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 1324 optimal weight: 5.9990 chunk 902 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 1183 optimal weight: 8.9990 chunk 656 optimal weight: 0.0770 chunk 1356 optimal weight: 9.9990 chunk 1099 optimal weight: 20.0000 chunk 1 optimal weight: 0.2980 chunk 811 optimal weight: 20.0000 chunk 1427 optimal weight: 5.9990 chunk 401 optimal weight: 1.9990 overall best weight: 2.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 446 GLN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1688 HIS ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3851 ASN ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1640 HIS ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A3889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4223 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4987 ASN D4020 GLN ** D4707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J3851 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 108088 Z= 0.247 Angle : 0.497 14.779 148544 Z= 0.252 Chirality : 0.038 0.270 18253 Planarity : 0.003 0.067 19495 Dihedral : 4.063 82.811 17196 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.77 % Allowed : 27.54 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.69 (0.07), residues: 16088 helix: 3.10 (0.05), residues: 9196 sheet: -0.62 (0.14), residues: 1375 loop : 0.13 (0.08), residues: 5517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1104 HIS 0.010 0.001 HIS A 218 PHE 0.026 0.001 PHE L 69 TYR 0.022 0.001 TYR J4849 ARG 0.009 0.000 ARG G2458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 1062 time to evaluate : 7.849 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: G 194 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6436 (p) REVERT: G 601 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: G 1494 MET cc_start: 0.7385 (mpp) cc_final: 0.6616 (mpp) REVERT: G 1760 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.7025 (t-170) REVERT: G 2197 LEU cc_start: 0.8892 (tp) cc_final: 0.8661 (tt) REVERT: G 2198 MET cc_start: 0.8786 (mmm) cc_final: 0.8369 (mmm) REVERT: G 2203 MET cc_start: 0.7993 (mpp) cc_final: 0.7233 (mtm) REVERT: G 2384 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7936 (tp) REVERT: G 2664 PHE cc_start: 0.8066 (m-80) cc_final: 0.7334 (t80) REVERT: G 3723 MET cc_start: 0.8988 (mmt) cc_final: 0.8641 (mmt) REVERT: G 3817 LEU cc_start: 0.9014 (tp) cc_final: 0.8724 (tp) REVERT: G 3967 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6937 (mm-30) REVERT: G 4066 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8491 (tt) REVERT: G 4956 THR cc_start: 0.8851 (t) cc_final: 0.8605 (t) REVERT: G 4992 LEU cc_start: 0.8922 (tp) cc_final: 0.8593 (tt) REVERT: G 5001 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8710 (p) REVERT: A 483 MET cc_start: 0.7929 (ppp) cc_final: 0.7641 (ppp) REVERT: A 1522 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5129 (mm) REVERT: A 1865 MET cc_start: 0.8128 (ppp) cc_final: 0.7636 (ppp) REVERT: A 1958 LEU cc_start: 0.9089 (tp) cc_final: 0.8818 (tp) REVERT: A 3721 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 3723 MET cc_start: 0.8184 (mmp) cc_final: 0.7689 (mmt) REVERT: A 3844 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7997 (mm) REVERT: A 4064 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7727 (pmm) REVERT: A 4639 MET cc_start: 0.7876 (mmt) cc_final: 0.7556 (mmt) REVERT: A 4874 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8156 (mmp) REVERT: D 148 TRP cc_start: 0.6676 (m100) cc_final: 0.6340 (m100) REVERT: D 2290 LEU cc_start: 0.9114 (tp) cc_final: 0.8816 (mt) REVERT: D 2696 TYR cc_start: 0.4922 (m-80) cc_final: 0.4487 (m-80) REVERT: D 3927 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 4023 MET cc_start: 0.7849 (ttp) cc_final: 0.7586 (ttp) REVERT: D 4183 ILE cc_start: 0.8669 (mm) cc_final: 0.8436 (mt) REVERT: D 4565 LEU cc_start: 0.9241 (tp) cc_final: 0.9024 (tp) REVERT: D 4580 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.6585 (t80) REVERT: J 447 ASP cc_start: 0.8709 (t0) cc_final: 0.8503 (t0) REVERT: J 478 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.6811 (t80) REVERT: J 1494 MET cc_start: 0.7523 (mmm) cc_final: 0.7246 (mmm) REVERT: J 1500 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6424 (p90) REVERT: J 1659 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8905 (mm) REVERT: J 1939 MET cc_start: 0.8380 (mmm) cc_final: 0.8008 (mtt) REVERT: J 2198 MET cc_start: 0.8324 (tpp) cc_final: 0.8099 (tpp) REVERT: J 2228 MET cc_start: 0.8356 (ppp) cc_final: 0.8112 (tmm) REVERT: J 2312 MET cc_start: 0.7286 (ppp) cc_final: 0.6148 (ptt) REVERT: J 2546 MET cc_start: 0.7603 (tpp) cc_final: 0.6889 (tpp) REVERT: J 3652 MET cc_start: 0.8192 (mtm) cc_final: 0.7720 (mtm) REVERT: J 3979 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8839 (t) REVERT: J 4103 PHE cc_start: 0.2108 (OUTLIER) cc_final: 0.1544 (m-80) REVERT: K 35 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8138 (mtmt) REVERT: K 41 ASP cc_start: 0.8371 (m-30) cc_final: 0.8136 (m-30) outliers start: 401 outliers final: 287 residues processed: 1386 average time/residue: 0.7866 time to fit residues: 2017.2092 Evaluate side-chains 1334 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1029 time to evaluate : 8.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 720 HIS Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 781 VAL Chi-restraints excluded: chain G residue 789 VAL Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1430 THR Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1454 THR Chi-restraints excluded: chain G residue 1500 PHE Chi-restraints excluded: chain G residue 1548 LEU Chi-restraints excluded: chain G residue 1553 PHE Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1654 SER Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1760 HIS Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 1955 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 2627 VAL Chi-restraints excluded: chain G residue 3667 HIS Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3698 LEU Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3708 THR Chi-restraints excluded: chain G residue 3721 LEU Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3771 HIS Chi-restraints excluded: chain G residue 3804 ILE Chi-restraints excluded: chain G residue 3910 THR Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4066 LEU Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4241 THR Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4556 SER Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4628 VAL Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4658 ILE Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4708 THR Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain G residue 4801 LEU Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4914 VAL Chi-restraints excluded: chain G residue 4931 ILE Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain G residue 5001 THR Chi-restraints excluded: chain G residue 5027 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1640 HIS Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1716 ILE Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1842 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3844 LEU Chi-restraints excluded: chain A residue 3905 THR Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4064 MET Chi-restraints excluded: chain A residue 4181 ILE Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4577 LEU Chi-restraints excluded: chain A residue 4582 VAL Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4874 MET Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4915 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1695 LEU Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1717 SER Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 2596 THR Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 3844 LEU Chi-restraints excluded: chain D residue 3916 ILE Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4740 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4915 VAL Chi-restraints excluded: chain D residue 4925 ILE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 536 ASN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 563 VAL Chi-restraints excluded: chain J residue 588 SER Chi-restraints excluded: chain J residue 605 SER Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 642 THR Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 767 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1123 VAL Chi-restraints excluded: chain J residue 1139 PHE Chi-restraints excluded: chain J residue 1158 ASN Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1430 THR Chi-restraints excluded: chain J residue 1431 THR Chi-restraints excluded: chain J residue 1432 THR Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1520 VAL Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1659 LEU Chi-restraints excluded: chain J residue 1715 LEU Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1771 LEU Chi-restraints excluded: chain J residue 1846 SER Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2152 THR Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2186 MET Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2280 VAL Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3017 PHE Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3721 LEU Chi-restraints excluded: chain J residue 3732 SER Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3937 TYR Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 3989 VAL Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4055 VAL Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4651 THR Chi-restraints excluded: chain J residue 4686 LEU Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4801 LEU Chi-restraints excluded: chain J residue 4803 HIS Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4850 LEU Chi-restraints excluded: chain J residue 4876 CYS Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4950 VAL Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 534 optimal weight: 9.9990 chunk 1431 optimal weight: 0.2980 chunk 314 optimal weight: 2.9990 chunk 933 optimal weight: 0.7980 chunk 392 optimal weight: 0.9980 chunk 1591 optimal weight: 1.9990 chunk 1321 optimal weight: 20.0000 chunk 736 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 526 optimal weight: 7.9990 chunk 835 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1688 HIS ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3851 ASN ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A1206 GLN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4857 ASN ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN D4707 ASN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3851 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 108088 Z= 0.138 Angle : 0.478 13.654 148544 Z= 0.236 Chirality : 0.037 0.265 18253 Planarity : 0.003 0.064 19495 Dihedral : 3.942 81.495 17194 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.14 % Allowed : 29.35 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.80 (0.07), residues: 16088 helix: 3.18 (0.05), residues: 9204 sheet: -0.46 (0.15), residues: 1332 loop : 0.15 (0.08), residues: 5552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 702 HIS 0.045 0.001 HIS A1640 PHE 0.026 0.001 PHE A3996 TYR 0.037 0.001 TYR G1712 ARG 0.007 0.000 ARG J 595 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1103 time to evaluate : 8.531 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: G 194 SER cc_start: 0.6632 (OUTLIER) cc_final: 0.6350 (p) REVERT: G 1494 MET cc_start: 0.7056 (mpp) cc_final: 0.6240 (mpp) REVERT: G 1563 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7176 (pp30) REVERT: G 2198 MET cc_start: 0.8693 (mmm) cc_final: 0.8337 (mmm) REVERT: G 2203 MET cc_start: 0.8012 (mpp) cc_final: 0.7407 (mpp) REVERT: G 2384 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7946 (tp) REVERT: G 2451 LEU cc_start: 0.8732 (pp) cc_final: 0.8478 (mm) REVERT: G 2664 PHE cc_start: 0.8005 (m-80) cc_final: 0.7338 (t80) REVERT: G 3667 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7199 (p90) REVERT: G 3723 MET cc_start: 0.8958 (mmt) cc_final: 0.8701 (mmt) REVERT: G 3817 LEU cc_start: 0.8849 (tp) cc_final: 0.8524 (tp) REVERT: G 3836 MET cc_start: 0.8207 (ttm) cc_final: 0.7925 (ttp) REVERT: G 3856 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8269 (mm) REVERT: G 3967 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6646 (mm-30) REVERT: G 4066 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8465 (tt) REVERT: G 4251 ILE cc_start: 0.9388 (pt) cc_final: 0.9029 (mm) REVERT: G 4956 THR cc_start: 0.8794 (t) cc_final: 0.8537 (t) REVERT: A 1522 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5017 (mm) REVERT: A 1865 MET cc_start: 0.8136 (ppp) cc_final: 0.7756 (ppp) REVERT: A 1958 LEU cc_start: 0.9116 (tp) cc_final: 0.8829 (tp) REVERT: A 3721 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7909 (tp) REVERT: A 3723 MET cc_start: 0.8047 (mmp) cc_final: 0.7654 (mmt) REVERT: A 4064 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7786 (pmm) REVERT: A 4815 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8129 (t0) REVERT: D 148 TRP cc_start: 0.6586 (m100) cc_final: 0.6260 (m100) REVERT: D 2208 MET cc_start: 0.8090 (mtp) cc_final: 0.7586 (ttm) REVERT: D 2290 LEU cc_start: 0.9117 (tp) cc_final: 0.8893 (mt) REVERT: D 2696 TYR cc_start: 0.5034 (m-80) cc_final: 0.4628 (m-80) REVERT: D 3927 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 4023 MET cc_start: 0.7795 (ttp) cc_final: 0.7557 (ttp) REVERT: D 4580 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.6303 (t80) REVERT: D 4652 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8545 (tp) REVERT: J 447 ASP cc_start: 0.8656 (t0) cc_final: 0.8452 (t0) REVERT: J 478 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6825 (t80) REVERT: J 1494 MET cc_start: 0.7151 (mmm) cc_final: 0.6912 (mmm) REVERT: J 1500 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6322 (p90) REVERT: J 1659 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8812 (mm) REVERT: J 2198 MET cc_start: 0.8318 (tpp) cc_final: 0.8032 (tpp) REVERT: J 2211 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7720 (tmm) REVERT: J 2228 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7889 (tmm) REVERT: J 2312 MET cc_start: 0.7229 (ppp) cc_final: 0.5877 (ptt) REVERT: J 2546 MET cc_start: 0.7600 (tpp) cc_final: 0.6970 (tpp) REVERT: J 3926 LEU cc_start: 0.8866 (tt) cc_final: 0.8619 (tt) REVERT: J 3979 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8792 (t) REVERT: J 4103 PHE cc_start: 0.2175 (OUTLIER) cc_final: 0.1531 (m-80) outliers start: 287 outliers final: 198 residues processed: 1325 average time/residue: 0.7869 time to fit residues: 1931.9810 Evaluate side-chains 1278 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1061 time to evaluate : 8.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 600 LEU Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1500 PHE Chi-restraints excluded: chain G residue 1548 LEU Chi-restraints excluded: chain G residue 1553 PHE Chi-restraints excluded: chain G residue 1563 GLN Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1654 SER Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 1939 MET Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2553 TYR Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 2627 VAL Chi-restraints excluded: chain G residue 3667 HIS Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3732 SER Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3856 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4051 SER Chi-restraints excluded: chain G residue 4066 LEU Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4628 VAL Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4681 LEU Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4820 VAL Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1842 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2142 TYR Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2420 HIS Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3905 THR Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4064 MET Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4815 ASP Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1721 GLU Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2326 CYS Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 3844 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4652 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1123 VAL Chi-restraints excluded: chain J residue 1139 PHE Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1432 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1608 MET Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1659 LEU Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1771 LEU Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2131 LEU Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2211 MET Chi-restraints excluded: chain J residue 2228 MET Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3017 PHE Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3721 LEU Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3951 PHE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4657 CYS Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4803 HIS Chi-restraints excluded: chain J residue 4876 CYS Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 1534 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 906 optimal weight: 10.0000 chunk 1162 optimal weight: 0.9980 chunk 900 optimal weight: 10.0000 chunk 1339 optimal weight: 0.5980 chunk 888 optimal weight: 40.0000 chunk 1585 optimal weight: 0.9980 chunk 992 optimal weight: 0.0980 chunk 966 optimal weight: 6.9990 chunk 732 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1688 HIS ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4574 ASN A 639 ASN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN A4223 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 HIS J3851 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 108088 Z= 0.143 Angle : 0.480 13.629 148544 Z= 0.235 Chirality : 0.037 0.217 18253 Planarity : 0.003 0.061 19495 Dihedral : 3.875 80.560 17194 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.11 % Allowed : 29.33 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.82 (0.07), residues: 16088 helix: 3.20 (0.05), residues: 9203 sheet: -0.44 (0.15), residues: 1330 loop : 0.17 (0.09), residues: 5555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 200 HIS 0.010 0.001 HIS G3771 PHE 0.071 0.001 PHE A3996 TYR 0.032 0.001 TYR G1712 ARG 0.006 0.000 ARG J 595 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1083 time to evaluate : 9.045 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: G 194 SER cc_start: 0.6608 (OUTLIER) cc_final: 0.6339 (p) REVERT: G 1494 MET cc_start: 0.7074 (mpp) cc_final: 0.6233 (mpp) REVERT: G 2198 MET cc_start: 0.8523 (mmm) cc_final: 0.8303 (mmm) REVERT: G 2451 LEU cc_start: 0.8711 (pp) cc_final: 0.8480 (mm) REVERT: G 2664 PHE cc_start: 0.8011 (m-80) cc_final: 0.7336 (t80) REVERT: G 3723 MET cc_start: 0.8937 (mmt) cc_final: 0.8620 (mmt) REVERT: G 3817 LEU cc_start: 0.8818 (tp) cc_final: 0.8499 (tp) REVERT: G 3836 MET cc_start: 0.8160 (ttm) cc_final: 0.7913 (ttp) REVERT: G 3967 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6599 (mm-30) REVERT: G 4066 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8476 (tt) REVERT: G 4233 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9013 (mm) REVERT: G 4251 ILE cc_start: 0.9376 (pt) cc_final: 0.9024 (mm) REVERT: G 4574 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8469 (m-40) REVERT: G 4956 THR cc_start: 0.8778 (t) cc_final: 0.8510 (t) REVERT: A 1522 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5003 (mm) REVERT: A 1549 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: A 1865 MET cc_start: 0.8111 (ppp) cc_final: 0.7752 (ppp) REVERT: A 1958 LEU cc_start: 0.9106 (tp) cc_final: 0.8835 (tp) REVERT: A 2097 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7594 (tp) REVERT: A 3723 MET cc_start: 0.8127 (mmp) cc_final: 0.7624 (mmt) REVERT: A 3927 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 4064 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7769 (pmm) REVERT: A 4815 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8112 (t0) REVERT: D 2288 LEU cc_start: 0.9200 (tp) cc_final: 0.8997 (tt) REVERT: D 2290 LEU cc_start: 0.9116 (tp) cc_final: 0.8896 (mt) REVERT: D 2696 TYR cc_start: 0.5108 (m-80) cc_final: 0.4816 (m-80) REVERT: D 4580 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.6169 (t80) REVERT: J 447 ASP cc_start: 0.8633 (t0) cc_final: 0.8422 (t0) REVERT: J 478 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6812 (t80) REVERT: J 1494 MET cc_start: 0.7155 (mmm) cc_final: 0.6937 (mmm) REVERT: J 1500 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6369 (p90) REVERT: J 1659 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8818 (mm) REVERT: J 1939 MET cc_start: 0.8217 (mmm) cc_final: 0.7960 (mtt) REVERT: J 2105 TRP cc_start: 0.8321 (m-10) cc_final: 0.7851 (m-10) REVERT: J 2198 MET cc_start: 0.8321 (tpp) cc_final: 0.8023 (tpp) REVERT: J 2228 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7889 (tmm) REVERT: J 2312 MET cc_start: 0.7201 (ppp) cc_final: 0.5820 (ptt) REVERT: J 2530 MET cc_start: 0.7260 (ppp) cc_final: 0.6933 (ppp) REVERT: J 2546 MET cc_start: 0.7530 (tpp) cc_final: 0.6880 (tpp) REVERT: J 3652 MET cc_start: 0.8118 (mtm) cc_final: 0.7675 (mtm) REVERT: J 3979 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8806 (t) REVERT: J 4103 PHE cc_start: 0.2177 (OUTLIER) cc_final: 0.1522 (m-80) REVERT: J 4569 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8145 (tt) outliers start: 284 outliers final: 226 residues processed: 1310 average time/residue: 0.7777 time to fit residues: 1886.4385 Evaluate side-chains 1309 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1066 time to evaluate : 8.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 720 HIS Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 1127 HIS Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1500 PHE Chi-restraints excluded: chain G residue 1520 VAL Chi-restraints excluded: chain G residue 1548 LEU Chi-restraints excluded: chain G residue 1553 PHE Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1654 SER Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1848 LEU Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 1939 MET Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 2627 VAL Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3732 SER Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3910 THR Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4066 LEU Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4233 LEU Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4565 LEU Chi-restraints excluded: chain G residue 4574 ASN Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4628 VAL Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4681 LEU Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4820 VAL Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1492 CYS Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1842 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2420 HIS Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4064 MET Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4577 LEU Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4815 ASP Chi-restraints excluded: chain A residue 4823 LEU Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1721 GLU Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2326 CYS Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 2596 THR Chi-restraints excluded: chain D residue 3733 CYS Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 3844 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4668 LEU Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 113 HIS Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1123 VAL Chi-restraints excluded: chain J residue 1139 PHE Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1608 MET Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1659 LEU Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1830 VAL Chi-restraints excluded: chain J residue 1848 LEU Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2131 LEU Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2228 MET Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3017 PHE Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3732 SER Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3937 TYR Chi-restraints excluded: chain J residue 3951 PHE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4569 LEU Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4657 CYS Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4803 HIS Chi-restraints excluded: chain J residue 4876 CYS Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 980 optimal weight: 4.9990 chunk 633 optimal weight: 10.0000 chunk 946 optimal weight: 50.0000 chunk 477 optimal weight: 20.0000 chunk 311 optimal weight: 0.0000 chunk 307 optimal weight: 3.9990 chunk 1008 optimal weight: 7.9990 chunk 1080 optimal weight: 9.9990 chunk 783 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 1246 optimal weight: 30.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 465 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 647 ASN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2194 HIS ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1640 HIS ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN A3781 GLN A3851 ASN A3889 GLN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4987 ASN D1640 HIS D2253 HIS ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4700 GLN J 113 HIS ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1660 GLN J1663 HIS J3851 ASN J4216 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 108088 Z= 0.369 Angle : 0.603 17.966 148544 Z= 0.306 Chirality : 0.040 0.219 18253 Planarity : 0.004 0.065 19495 Dihedral : 4.192 83.419 17194 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.16 % Allowed : 28.51 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.07), residues: 16088 helix: 2.94 (0.05), residues: 9201 sheet: -0.64 (0.14), residues: 1342 loop : -0.00 (0.08), residues: 5545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G1104 HIS 0.020 0.001 HIS J 113 PHE 0.053 0.002 PHE A3996 TYR 0.027 0.002 TYR G2331 ARG 0.007 0.001 ARG A5017 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1015 time to evaluate : 9.291 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: G 194 SER cc_start: 0.6523 (OUTLIER) cc_final: 0.6281 (p) REVERT: G 601 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: G 1494 MET cc_start: 0.7188 (mpp) cc_final: 0.6590 (mpp) REVERT: G 1760 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7331 (t-170) REVERT: G 2203 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7836 (mtm) REVERT: G 2384 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7958 (tp) REVERT: G 2664 PHE cc_start: 0.8245 (m-80) cc_final: 0.7640 (t80) REVERT: G 3817 LEU cc_start: 0.9076 (tp) cc_final: 0.8848 (tt) REVERT: G 3967 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7042 (mm-30) REVERT: G 4066 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8620 (tt) REVERT: G 4233 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9161 (mm) REVERT: G 4574 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8536 (m110) REVERT: G 4956 THR cc_start: 0.8860 (t) cc_final: 0.8627 (t) REVERT: G 4992 LEU cc_start: 0.8980 (tp) cc_final: 0.8595 (tt) REVERT: A 1522 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5215 (mm) REVERT: A 1865 MET cc_start: 0.8067 (ppp) cc_final: 0.7583 (ppp) REVERT: A 2153 MET cc_start: 0.8442 (mmp) cc_final: 0.8220 (mmp) REVERT: A 4064 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7932 (pmm) REVERT: A 4639 MET cc_start: 0.7921 (mmt) cc_final: 0.7569 (mmt) REVERT: D 148 TRP cc_start: 0.6752 (m100) cc_final: 0.6351 (m100) REVERT: D 3928 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7699 (mm-30) REVERT: D 4028 LEU cc_start: 0.9140 (mm) cc_final: 0.8928 (mt) REVERT: D 4580 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.6636 (t80) REVERT: D 4652 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8637 (tp) REVERT: J 182 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8485 (tt) REVERT: J 478 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6949 (t80) REVERT: J 1500 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6584 (p90) REVERT: J 1659 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9035 (mm) REVERT: J 2198 MET cc_start: 0.8307 (tpp) cc_final: 0.7796 (tpp) REVERT: J 2312 MET cc_start: 0.7479 (ppp) cc_final: 0.6489 (ptt) REVERT: J 2530 MET cc_start: 0.7212 (ppp) cc_final: 0.6886 (ppp) REVERT: J 2546 MET cc_start: 0.7593 (tpp) cc_final: 0.6917 (tpp) REVERT: J 3652 MET cc_start: 0.8214 (mtm) cc_final: 0.7803 (mtm) REVERT: J 3979 SER cc_start: 0.9145 (OUTLIER) cc_final: 0.8882 (t) REVERT: J 4103 PHE cc_start: 0.2397 (OUTLIER) cc_final: 0.1829 (m-80) outliers start: 357 outliers final: 271 residues processed: 1303 average time/residue: 0.7564 time to fit residues: 1823.4647 Evaluate side-chains 1283 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 994 time to evaluate : 8.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 224 HIS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 597 HIS Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain G residue 609 CYS Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 720 HIS Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 1127 HIS Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1159 THR Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1430 THR Chi-restraints excluded: chain G residue 1454 THR Chi-restraints excluded: chain G residue 1500 PHE Chi-restraints excluded: chain G residue 1548 LEU Chi-restraints excluded: chain G residue 1553 PHE Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1760 HIS Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1848 LEU Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1858 ASP Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2182 ILE Chi-restraints excluded: chain G residue 2203 MET Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2368 LEU Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2553 TYR Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 2627 VAL Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3721 LEU Chi-restraints excluded: chain G residue 3732 SER Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3804 ILE Chi-restraints excluded: chain G residue 3910 THR Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4051 SER Chi-restraints excluded: chain G residue 4066 LEU Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4148 THR Chi-restraints excluded: chain G residue 4181 ILE Chi-restraints excluded: chain G residue 4233 LEU Chi-restraints excluded: chain G residue 4241 THR Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4574 ASN Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4628 VAL Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4658 ILE Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4820 VAL Chi-restraints excluded: chain G residue 4830 VAL Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1549 PHE Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1716 ILE Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2420 HIS Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3804 ILE Chi-restraints excluded: chain A residue 3892 CYS Chi-restraints excluded: chain A residue 3905 THR Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3921 ASP Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4064 MET Chi-restraints excluded: chain A residue 4181 ILE Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4577 LEU Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4915 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4932 ILE Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5010 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1695 LEU Chi-restraints excluded: chain D residue 1721 GLU Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2326 CYS Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 2596 THR Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4652 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4925 ILE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 536 ASN Chi-restraints excluded: chain J residue 563 VAL Chi-restraints excluded: chain J residue 587 ILE Chi-restraints excluded: chain J residue 605 SER Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1139 PHE Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1430 THR Chi-restraints excluded: chain J residue 1431 THR Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1608 MET Chi-restraints excluded: chain J residue 1613 LEU Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1650 ILE Chi-restraints excluded: chain J residue 1659 LEU Chi-restraints excluded: chain J residue 1660 GLN Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1830 VAL Chi-restraints excluded: chain J residue 1846 SER Chi-restraints excluded: chain J residue 1848 LEU Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2131 LEU Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2228 MET Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3017 PHE Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3732 SER Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4331 LEU Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4801 LEU Chi-restraints excluded: chain J residue 4827 LEU Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 1442 optimal weight: 0.0060 chunk 1518 optimal weight: 0.7980 chunk 1385 optimal weight: 0.4980 chunk 1477 optimal weight: 8.9990 chunk 889 optimal weight: 40.0000 chunk 643 optimal weight: 10.0000 chunk 1160 optimal weight: 0.6980 chunk 453 optimal weight: 9.9990 chunk 1335 optimal weight: 7.9990 chunk 1397 optimal weight: 3.9990 chunk 1472 optimal weight: 8.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 405 HIS G 465 GLN ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4574 ASN A1252 HIS ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1660 GLN J2169 GLN J3851 ASN K 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 108088 Z= 0.178 Angle : 0.522 14.711 148544 Z= 0.256 Chirality : 0.038 0.330 18253 Planarity : 0.003 0.062 19495 Dihedral : 4.054 83.997 17193 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.97 % Allowed : 30.13 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.64 (0.07), residues: 16088 helix: 3.08 (0.05), residues: 9198 sheet: -0.59 (0.14), residues: 1365 loop : 0.07 (0.09), residues: 5525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 722 HIS 0.010 0.001 HIS G3771 PHE 0.054 0.001 PHE A3996 TYR 0.030 0.001 TYR G2331 ARG 0.013 0.000 ARG J1661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1074 time to evaluate : 8.664 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: G 194 SER cc_start: 0.6599 (OUTLIER) cc_final: 0.6368 (p) REVERT: G 1494 MET cc_start: 0.6868 (mpp) cc_final: 0.6222 (mpp) REVERT: G 2128 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7155 (t80) REVERT: G 2198 MET cc_start: 0.8557 (mmm) cc_final: 0.8282 (mmm) REVERT: G 2384 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7984 (tp) REVERT: G 2502 MET cc_start: 0.8438 (mmp) cc_final: 0.8147 (mmp) REVERT: G 2664 PHE cc_start: 0.8155 (m-80) cc_final: 0.7522 (t80) REVERT: G 3817 LEU cc_start: 0.9015 (tp) cc_final: 0.8712 (tp) REVERT: G 3836 MET cc_start: 0.8198 (ttm) cc_final: 0.7944 (ttp) REVERT: G 3967 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6761 (mm-30) REVERT: G 3968 TYR cc_start: 0.8184 (m-80) cc_final: 0.7331 (m-80) REVERT: G 4066 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8559 (tt) REVERT: G 4233 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (mm) REVERT: G 4251 ILE cc_start: 0.9352 (pt) cc_final: 0.9060 (mm) REVERT: G 4956 THR cc_start: 0.8794 (t) cc_final: 0.8550 (t) REVERT: A 1522 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.4858 (mm) REVERT: A 1865 MET cc_start: 0.7973 (ppp) cc_final: 0.7427 (ptm) REVERT: A 3721 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 3967 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6540 (tp30) REVERT: A 4639 MET cc_start: 0.7912 (mmt) cc_final: 0.7562 (mmt) REVERT: D 148 TRP cc_start: 0.6746 (m100) cc_final: 0.6391 (m100) REVERT: D 3928 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 4028 LEU cc_start: 0.9075 (mm) cc_final: 0.8874 (mt) REVERT: D 4580 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.6438 (t80) REVERT: D 4652 LEU cc_start: 0.8954 (tp) cc_final: 0.8602 (tp) REVERT: J 182 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8394 (tt) REVERT: J 478 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6872 (t80) REVERT: J 1500 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6491 (p90) REVERT: J 2312 MET cc_start: 0.7394 (ppp) cc_final: 0.6284 (ptt) REVERT: J 2530 MET cc_start: 0.7160 (ppp) cc_final: 0.6864 (ppp) REVERT: J 2546 MET cc_start: 0.7536 (tpp) cc_final: 0.6849 (tpp) REVERT: J 3652 MET cc_start: 0.8169 (mtm) cc_final: 0.7732 (mtm) REVERT: J 3979 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8822 (t) REVERT: J 4103 PHE cc_start: 0.2373 (OUTLIER) cc_final: 0.1809 (m-80) outliers start: 274 outliers final: 230 residues processed: 1293 average time/residue: 0.8442 time to fit residues: 2025.2001 Evaluate side-chains 1278 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1035 time to evaluate : 8.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 213 TYR Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 720 HIS Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 1127 HIS Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1159 THR Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1454 THR Chi-restraints excluded: chain G residue 1500 PHE Chi-restraints excluded: chain G residue 1548 LEU Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1848 LEU Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2203 MET Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2463 LEU Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2553 TYR Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 2627 VAL Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3732 SER Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3924 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4066 LEU Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4233 LEU Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4628 VAL Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4708 THR Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1842 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2420 HIS Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3905 THR Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4577 LEU Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1695 LEU Chi-restraints excluded: chain D residue 1721 GLU Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2326 CYS Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 2596 THR Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 605 SER Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1139 PHE Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1430 THR Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1660 GLN Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1830 VAL Chi-restraints excluded: chain J residue 1848 LEU Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2131 LEU Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2228 MET Chi-restraints excluded: chain J residue 2257 LEU Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3017 PHE Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3732 SER Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4803 HIS Chi-restraints excluded: chain J residue 4876 CYS Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 970 optimal weight: 0.3980 chunk 1562 optimal weight: 20.0000 chunk 953 optimal weight: 4.9990 chunk 741 optimal weight: 20.0000 chunk 1086 optimal weight: 3.9990 chunk 1638 optimal weight: 3.9990 chunk 1508 optimal weight: 20.0000 chunk 1305 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 1008 optimal weight: 8.9990 chunk 800 optimal weight: 8.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G4204 GLN ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4987 ASN ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1660 GLN J3851 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 108088 Z= 0.285 Angle : 0.563 15.368 148544 Z= 0.279 Chirality : 0.039 0.404 18253 Planarity : 0.003 0.064 19495 Dihedral : 4.094 85.356 17191 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.95 % Allowed : 30.18 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.53 (0.07), residues: 16088 helix: 2.99 (0.05), residues: 9204 sheet: -0.63 (0.14), residues: 1367 loop : 0.02 (0.08), residues: 5517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP G 722 HIS 0.009 0.001 HIS G3771 PHE 0.047 0.002 PHE A3996 TYR 0.031 0.002 TYR G3722 ARG 0.008 0.000 ARG A5017 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32176 Ramachandran restraints generated. 16088 Oldfield, 0 Emsley, 16088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1021 time to evaluate : 8.483 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: G 194 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.6358 (p) REVERT: G 601 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: G 1494 MET cc_start: 0.6968 (mpp) cc_final: 0.6422 (mpp) REVERT: G 1636 MET cc_start: 0.8005 (ttp) cc_final: 0.7796 (ppp) REVERT: G 2203 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: G 2384 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7916 (tp) REVERT: G 2502 MET cc_start: 0.8538 (mmp) cc_final: 0.8206 (mmp) REVERT: G 2664 PHE cc_start: 0.8225 (m-80) cc_final: 0.7640 (t80) REVERT: G 3817 LEU cc_start: 0.9033 (tp) cc_final: 0.8758 (tt) REVERT: G 3912 THR cc_start: 0.8247 (m) cc_final: 0.7780 (p) REVERT: G 3967 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6916 (mm-30) REVERT: G 4066 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8546 (tt) REVERT: G 4233 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9128 (mm) REVERT: G 4251 ILE cc_start: 0.9381 (pt) cc_final: 0.9075 (mm) REVERT: G 4879 MET cc_start: 0.8796 (tpt) cc_final: 0.8489 (tpp) REVERT: G 4956 THR cc_start: 0.8821 (t) cc_final: 0.8587 (t) REVERT: G 4992 LEU cc_start: 0.8967 (tp) cc_final: 0.8520 (tt) REVERT: A 1522 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5056 (mm) REVERT: A 1865 MET cc_start: 0.7971 (ppp) cc_final: 0.7608 (ptm) REVERT: A 4639 MET cc_start: 0.7921 (mmt) cc_final: 0.7551 (mmt) REVERT: A 4954 MET cc_start: 0.7930 (mmp) cc_final: 0.7596 (mmp) REVERT: B 30 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7430 (tt) REVERT: D 148 TRP cc_start: 0.6765 (m100) cc_final: 0.6382 (m100) REVERT: D 3673 MET cc_start: 0.8273 (mmp) cc_final: 0.7874 (tpp) REVERT: D 4028 LEU cc_start: 0.9136 (mm) cc_final: 0.8929 (mt) REVERT: D 4580 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.6484 (t80) REVERT: D 4652 LEU cc_start: 0.8998 (tp) cc_final: 0.8656 (tp) REVERT: J 182 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (tt) REVERT: J 478 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.6913 (t80) REVERT: J 1500 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6644 (p90) REVERT: J 1659 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9004 (mm) REVERT: J 1814 MET cc_start: 0.7706 (mmm) cc_final: 0.7269 (tmm) REVERT: J 1844 LEU cc_start: 0.9082 (tp) cc_final: 0.8828 (tt) REVERT: J 2198 MET cc_start: 0.8261 (tpp) cc_final: 0.7943 (tpp) REVERT: J 2312 MET cc_start: 0.7520 (ppp) cc_final: 0.6493 (ptt) REVERT: J 2530 MET cc_start: 0.7174 (ppp) cc_final: 0.6883 (ppp) REVERT: J 2546 MET cc_start: 0.7695 (tpp) cc_final: 0.7001 (tpp) REVERT: J 3652 MET cc_start: 0.8217 (mtm) cc_final: 0.7795 (mtm) REVERT: J 3979 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8833 (t) REVERT: J 4103 PHE cc_start: 0.2561 (OUTLIER) cc_final: 0.1995 (m-80) outliers start: 273 outliers final: 239 residues processed: 1245 average time/residue: 0.8560 time to fit residues: 1981.3393 Evaluate side-chains 1265 residues out of total 14399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1011 time to evaluate : 8.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 571 SER Chi-restraints excluded: chain G residue 590 LEU Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain G residue 609 CYS Chi-restraints excluded: chain G residue 625 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 680 THR Chi-restraints excluded: chain G residue 720 HIS Chi-restraints excluded: chain G residue 752 VAL Chi-restraints excluded: chain G residue 757 PHE Chi-restraints excluded: chain G residue 1127 HIS Chi-restraints excluded: chain G residue 1148 VAL Chi-restraints excluded: chain G residue 1155 LEU Chi-restraints excluded: chain G residue 1159 THR Chi-restraints excluded: chain G residue 1177 THR Chi-restraints excluded: chain G residue 1189 LEU Chi-restraints excluded: chain G residue 1454 THR Chi-restraints excluded: chain G residue 1500 PHE Chi-restraints excluded: chain G residue 1548 LEU Chi-restraints excluded: chain G residue 1604 SER Chi-restraints excluded: chain G residue 1615 VAL Chi-restraints excluded: chain G residue 1657 LEU Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1703 LEU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1742 THR Chi-restraints excluded: chain G residue 1848 LEU Chi-restraints excluded: chain G residue 1850 VAL Chi-restraints excluded: chain G residue 1931 LEU Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2131 LEU Chi-restraints excluded: chain G residue 2138 LEU Chi-restraints excluded: chain G residue 2203 MET Chi-restraints excluded: chain G residue 2305 CYS Chi-restraints excluded: chain G residue 2384 ILE Chi-restraints excluded: chain G residue 2423 MET Chi-restraints excluded: chain G residue 2463 LEU Chi-restraints excluded: chain G residue 2506 LEU Chi-restraints excluded: chain G residue 2518 LEU Chi-restraints excluded: chain G residue 2553 TYR Chi-restraints excluded: chain G residue 2582 MET Chi-restraints excluded: chain G residue 2613 TYR Chi-restraints excluded: chain G residue 2627 VAL Chi-restraints excluded: chain G residue 3696 ASP Chi-restraints excluded: chain G residue 3698 LEU Chi-restraints excluded: chain G residue 3701 LEU Chi-restraints excluded: chain G residue 3708 THR Chi-restraints excluded: chain G residue 3732 SER Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3770 LEU Chi-restraints excluded: chain G residue 3913 ILE Chi-restraints excluded: chain G residue 3923 LEU Chi-restraints excluded: chain G residue 3924 LEU Chi-restraints excluded: chain G residue 3926 LEU Chi-restraints excluded: chain G residue 3937 TYR Chi-restraints excluded: chain G residue 3974 THR Chi-restraints excluded: chain G residue 3980 LEU Chi-restraints excluded: chain G residue 3983 SER Chi-restraints excluded: chain G residue 4034 ASN Chi-restraints excluded: chain G residue 4066 LEU Chi-restraints excluded: chain G residue 4081 VAL Chi-restraints excluded: chain G residue 4103 PHE Chi-restraints excluded: chain G residue 4128 PHE Chi-restraints excluded: chain G residue 4233 LEU Chi-restraints excluded: chain G residue 4544 LEU Chi-restraints excluded: chain G residue 4580 TYR Chi-restraints excluded: chain G residue 4628 VAL Chi-restraints excluded: chain G residue 4645 CYS Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4651 THR Chi-restraints excluded: chain G residue 4666 VAL Chi-restraints excluded: chain G residue 4708 THR Chi-restraints excluded: chain G residue 4773 VAL Chi-restraints excluded: chain G residue 4814 LEU Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4958 CYS Chi-restraints excluded: chain G residue 4980 LEU Chi-restraints excluded: chain G residue 4993 MET Chi-restraints excluded: chain G residue 5027 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1254 HIS Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1522 LEU Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1647 CYS Chi-restraints excluded: chain A residue 1674 CYS Chi-restraints excluded: chain A residue 1718 ILE Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1934 SER Chi-restraints excluded: chain A residue 1966 VAL Chi-restraints excluded: chain A residue 1969 LEU Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2135 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2253 HIS Chi-restraints excluded: chain A residue 2420 HIS Chi-restraints excluded: chain A residue 2569 PHE Chi-restraints excluded: chain A residue 3667 HIS Chi-restraints excluded: chain A residue 3721 LEU Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3817 LEU Chi-restraints excluded: chain A residue 3905 THR Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3974 THR Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4334 LEU Chi-restraints excluded: chain A residue 4577 LEU Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4681 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1695 LEU Chi-restraints excluded: chain D residue 1721 GLU Chi-restraints excluded: chain D residue 2240 CYS Chi-restraints excluded: chain D residue 2246 ASN Chi-restraints excluded: chain D residue 2295 LEU Chi-restraints excluded: chain D residue 2302 LEU Chi-restraints excluded: chain D residue 2326 CYS Chi-restraints excluded: chain D residue 2457 LEU Chi-restraints excluded: chain D residue 2596 THR Chi-restraints excluded: chain D residue 3829 PHE Chi-restraints excluded: chain D residue 3836 MET Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4858 PHE Chi-restraints excluded: chain D residue 4915 VAL Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 285 VAL Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 478 PHE Chi-restraints excluded: chain J residue 525 LEU Chi-restraints excluded: chain J residue 605 SER Chi-restraints excluded: chain J residue 631 LEU Chi-restraints excluded: chain J residue 666 VAL Chi-restraints excluded: chain J residue 702 TRP Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 752 VAL Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain J residue 1072 VAL Chi-restraints excluded: chain J residue 1139 PHE Chi-restraints excluded: chain J residue 1189 LEU Chi-restraints excluded: chain J residue 1266 THR Chi-restraints excluded: chain J residue 1430 THR Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1500 PHE Chi-restraints excluded: chain J residue 1516 ILE Chi-restraints excluded: chain J residue 1527 MET Chi-restraints excluded: chain J residue 1615 VAL Chi-restraints excluded: chain J residue 1659 LEU Chi-restraints excluded: chain J residue 1736 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1830 VAL Chi-restraints excluded: chain J residue 1846 SER Chi-restraints excluded: chain J residue 1848 LEU Chi-restraints excluded: chain J residue 1851 MET Chi-restraints excluded: chain J residue 1927 LEU Chi-restraints excluded: chain J residue 1966 VAL Chi-restraints excluded: chain J residue 2117 VAL Chi-restraints excluded: chain J residue 2123 LEU Chi-restraints excluded: chain J residue 2128 TYR Chi-restraints excluded: chain J residue 2131 LEU Chi-restraints excluded: chain J residue 2158 CYS Chi-restraints excluded: chain J residue 2194 HIS Chi-restraints excluded: chain J residue 2228 MET Chi-restraints excluded: chain J residue 2257 LEU Chi-restraints excluded: chain J residue 2335 LEU Chi-restraints excluded: chain J residue 2424 SER Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3017 PHE Chi-restraints excluded: chain J residue 3677 LEU Chi-restraints excluded: chain J residue 3706 SER Chi-restraints excluded: chain J residue 3732 SER Chi-restraints excluded: chain J residue 3764 LEU Chi-restraints excluded: chain J residue 3771 HIS Chi-restraints excluded: chain J residue 3836 MET Chi-restraints excluded: chain J residue 3897 ASN Chi-restraints excluded: chain J residue 3913 ILE Chi-restraints excluded: chain J residue 3979 SER Chi-restraints excluded: chain J residue 4029 SER Chi-restraints excluded: chain J residue 4103 PHE Chi-restraints excluded: chain J residue 4571 PHE Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4720 VAL Chi-restraints excluded: chain J residue 4792 LEU Chi-restraints excluded: chain J residue 4911 LEU Chi-restraints excluded: chain J residue 4998 LYS Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 73 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1645 random chunks: chunk 1036 optimal weight: 20.0000 chunk 1390 optimal weight: 0.7980 chunk 399 optimal weight: 3.9990 chunk 1203 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 1307 optimal weight: 3.9990 chunk 547 optimal weight: 0.0570 chunk 1342 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 465 GLN G1837 GLN ** G2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3851 ASN ** G4130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4223 ASN ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4987 ASN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 639 ASN J 681 HIS J1563 GLN J3851 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.105686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.078789 restraints weight = 414784.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078935 restraints weight = 226876.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.079409 restraints weight = 154793.073| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 108088 Z= 0.158 Angle : 0.527 15.584 148544 Z= 0.255 Chirality : 0.037 0.320 18253 Planarity : 0.003 0.063 19495 Dihedral : 3.982 85.452 17191 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.65 % Allowed : 30.59 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.65 (0.07), residues: 16088 helix: 3.08 (0.05), residues: 9196 sheet: -0.60 (0.14), residues: 1385 loop : 0.09 (0.09), residues: 5507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 722 HIS 0.012 0.001 HIS G3771 PHE 0.047 0.001 PHE A3996 TYR 0.038 0.001 TYR G2331 ARG 0.006 0.000 ARG J 595 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29750.59 seconds wall clock time: 514 minutes 29.90 seconds (30869.90 seconds total)