Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 00:12:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdi_25830/04_2023/7tdi_25830_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdi_25830/04_2023/7tdi_25830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdi_25830/04_2023/7tdi_25830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdi_25830/04_2023/7tdi_25830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdi_25830/04_2023/7tdi_25830_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdi_25830/04_2023/7tdi_25830_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 12 5.49 5 S 628 5.16 5 C 74108 2.51 5 N 20744 2.21 5 O 21628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 947": "OE1" <-> "OE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "B GLU 1157": "OE1" <-> "OE2" Residue "B GLU 1183": "OE1" <-> "OE2" Residue "B GLU 1652": "OE1" <-> "OE2" Residue "B GLU 1699": "OE1" <-> "OE2" Residue "B GLU 2205": "OE1" <-> "OE2" Residue "B GLU 2209": "OE1" <-> "OE2" Residue "B GLU 2348": "OE1" <-> "OE2" Residue "B GLU 3712": "OE1" <-> "OE2" Residue "B GLU 3718": "OE1" <-> "OE2" Residue "B GLU 3757": "OE1" <-> "OE2" Residue "B GLU 3789": "OE1" <-> "OE2" Residue "B GLU 3825": "OE1" <-> "OE2" Residue "B GLU 3848": "OE1" <-> "OE2" Residue "B GLU 3945": "OE1" <-> "OE2" Residue "B GLU 4011": "OE1" <-> "OE2" Residue "B GLU 4050": "OE1" <-> "OE2" Residue "B PHE 4061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4075": "OE1" <-> "OE2" Residue "B GLU 4107": "OE1" <-> "OE2" Residue "B GLU 4116": "OE1" <-> "OE2" Residue "B GLU 4127": "OE1" <-> "OE2" Residue "B GLU 4134": "OE1" <-> "OE2" Residue "B GLU 4168": "OE1" <-> "OE2" Residue "B GLU 4182": "OE1" <-> "OE2" Residue "B GLU 4191": "OE1" <-> "OE2" Residue "B GLU 4196": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B GLU 4224": "OE1" <-> "OE2" Residue "B GLU 4232": "OE1" <-> "OE2" Residue "B GLU 4239": "OE1" <-> "OE2" Residue "B GLU 4690": "OE1" <-> "OE2" Residue "B GLU 4735": "OE1" <-> "OE2" Residue "B PHE 4784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4867": "OE1" <-> "OE2" Residue "B GLU 4900": "OE1" <-> "OE2" Residue "B GLU 4976": "OE1" <-> "OE2" Residue "B GLU 4981": "OE1" <-> "OE2" Residue "B GLU 4982": "OE1" <-> "OE2" Residue "B GLU 5016": "OE1" <-> "OE2" Residue "B GLU 5033": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C GLU 1108": "OE1" <-> "OE2" Residue "C GLU 1652": "OE1" <-> "OE2" Residue "C GLU 1699": "OE1" <-> "OE2" Residue "C GLU 1950": "OE1" <-> "OE2" Residue "C GLU 1956": "OE1" <-> "OE2" Residue "C GLU 2115": "OE1" <-> "OE2" Residue "C GLU 2209": "OE1" <-> "OE2" Residue "C GLU 2348": "OE1" <-> "OE2" Residue "C GLU 3712": "OE1" <-> "OE2" Residue "C GLU 3718": "OE1" <-> "OE2" Residue "C PHE 3753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3755": "OE1" <-> "OE2" Residue "C GLU 3757": "OE1" <-> "OE2" Residue "C GLU 3789": "OE1" <-> "OE2" Residue "C GLU 3848": "OE1" <-> "OE2" Residue "C TYR 3922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3945": "OE1" <-> "OE2" Residue "C GLU 4011": "OE1" <-> "OE2" Residue "C GLU 4015": "OE1" <-> "OE2" Residue "C GLU 4107": "OE1" <-> "OE2" Residue "C GLU 4116": "OE1" <-> "OE2" Residue "C ASP 4118": "OD1" <-> "OD2" Residue "C GLU 4127": "OE1" <-> "OE2" Residue "C GLU 4168": "OE1" <-> "OE2" Residue "C GLU 4172": "OE1" <-> "OE2" Residue "C GLU 4182": "OE1" <-> "OE2" Residue "C GLU 4191": "OE1" <-> "OE2" Residue "C GLU 4196": "OE1" <-> "OE2" Residue "C GLU 4232": "OE1" <-> "OE2" Residue "C GLU 4239": "OE1" <-> "OE2" Residue "C GLU 4676": "OE1" <-> "OE2" Residue "C GLU 4682": "OE1" <-> "OE2" Residue "C GLU 4735": "OE1" <-> "OE2" Residue "C GLU 4867": "OE1" <-> "OE2" Residue "C GLU 4902": "OE1" <-> "OE2" Residue "C GLU 4942": "OE1" <-> "OE2" Residue "C GLU 4952": "OE1" <-> "OE2" Residue "C GLU 4982": "OE1" <-> "OE2" Residue "C GLU 5002": "OE1" <-> "OE2" Residue "C GLU 5016": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 517": "OE1" <-> "OE2" Residue "D GLU 630": "OE1" <-> "OE2" Residue "D GLU 1157": "OE1" <-> "OE2" Residue "D GLU 1183": "OE1" <-> "OE2" Residue "D GLU 1652": "OE1" <-> "OE2" Residue "D GLU 1956": "OE1" <-> "OE2" Residue "D GLU 1997": "OE1" <-> "OE2" Residue "D GLU 2347": "OE1" <-> "OE2" Residue "D GLU 2348": "OE1" <-> "OE2" Residue "D GLU 3712": "OE1" <-> "OE2" Residue "D GLU 3757": "OE1" <-> "OE2" Residue "D GLU 3777": "OE1" <-> "OE2" Residue "D GLU 3789": "OE1" <-> "OE2" Residue "D GLU 3811": "OE1" <-> "OE2" Residue "D GLU 3825": "OE1" <-> "OE2" Residue "D GLU 3945": "OE1" <-> "OE2" Residue "D GLU 4011": "OE1" <-> "OE2" Residue "D GLU 4050": "OE1" <-> "OE2" Residue "D GLU 4107": "OE1" <-> "OE2" Residue "D GLU 4116": "OE1" <-> "OE2" Residue "D GLU 4127": "OE1" <-> "OE2" Residue "D GLU 4134": "OE1" <-> "OE2" Residue "D GLU 4152": "OE1" <-> "OE2" Residue "D GLU 4165": "OE1" <-> "OE2" Residue "D GLU 4168": "OE1" <-> "OE2" Residue "D GLU 4172": "OE1" <-> "OE2" Residue "D GLU 4182": "OE1" <-> "OE2" Residue "D GLU 4196": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D GLU 4224": "OE1" <-> "OE2" Residue "D GLU 4239": "OE1" <-> "OE2" Residue "D PHE 4551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4690": "OE1" <-> "OE2" Residue "D GLU 4735": "OE1" <-> "OE2" Residue "D GLU 4867": "OE1" <-> "OE2" Residue "D GLU 5033": "OE1" <-> "OE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A GLU 1655": "OE1" <-> "OE2" Residue "A GLU 1699": "OE1" <-> "OE2" Residue "A GLU 1944": "OE1" <-> "OE2" Residue "A GLU 3665": "OE1" <-> "OE2" Residue "A GLU 3670": "OE1" <-> "OE2" Residue "A GLU 3750": "OE1" <-> "OE2" Residue "A GLU 3754": "OE1" <-> "OE2" Residue "A GLU 3757": "OE1" <-> "OE2" Residue "A GLU 3811": "OE1" <-> "OE2" Residue "A GLU 3825": "OE1" <-> "OE2" Residue "A GLU 3893": "OE1" <-> "OE2" Residue "A GLU 4011": "OE1" <-> "OE2" Residue "A GLU 4032": "OE1" <-> "OE2" Residue "A GLU 4056": "OE1" <-> "OE2" Residue "A GLU 4075": "OE1" <-> "OE2" Residue "A GLU 4107": "OE1" <-> "OE2" Residue "A GLU 4116": "OE1" <-> "OE2" Residue "A GLU 4134": "OE1" <-> "OE2" Residue "A GLU 4168": "OE1" <-> "OE2" Residue "A GLU 4196": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A GLU 4232": "OE1" <-> "OE2" Residue "A GLU 4244": "OE1" <-> "OE2" Residue "A GLU 4682": "OE1" <-> "OE2" Residue "A GLU 4735": "OE1" <-> "OE2" Residue "A GLU 4976": "OE1" <-> "OE2" Residue "A GLU 4981": "OE1" <-> "OE2" Residue "A GLU 5002": "OE1" <-> "OE2" Residue "A GLU 5016": "OE1" <-> "OE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 117132 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 29249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29249 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2878 Unresolved non-hydrogen angles: 4042 Unresolved non-hydrogen dihedrals: 1770 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1666 Chain: "C" Number of atoms: 29249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29249 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2878 Unresolved non-hydrogen angles: 4042 Unresolved non-hydrogen dihedrals: 1770 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1666 Chain: "D" Number of atoms: 29249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29249 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2878 Unresolved non-hydrogen angles: 4042 Unresolved non-hydrogen dihedrals: 1770 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1666 Chain: "A" Number of atoms: 29249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29249 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1199} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2878 Unresolved non-hydrogen angles: 4042 Unresolved non-hydrogen dihedrals: 1770 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1666 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28574 SG CYS B4958 181.646 180.966 102.651 1.00143.72 S ATOM 28599 SG CYS B4961 183.853 181.235 99.631 1.00137.93 S ATOM 57848 SG CYS C4961 206.730 184.289 99.822 1.00140.37 S ATOM 87072 SG CYS D4958 208.133 206.992 103.142 1.00161.73 S ATOM 87097 SG CYS D4961 205.580 207.375 100.209 1.00147.71 S ATOM A0CLD SG CYS A4958 181.315 207.590 102.562 1.00133.19 S ATOM A0CM2 SG CYS A4961 181.276 204.443 99.445 1.00120.45 S Time building chain proxies: 43.79, per 1000 atoms: 0.37 Number of scatterers: 117132 At special positions: 0 Unit cell: (390.065, 390.065, 193.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 628 16.00 P 12 15.00 O 21628 8.00 N 20744 7.00 C 74108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " 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: 33.58 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " Number of angles added : 4 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31360 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 472 helices and 60 sheets defined 54.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.91 Creating SS restraints... Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.435A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 249 through 256 removed outlier: 4.835A pdb=" N CYS B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 256' Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.934A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 4.008A pdb=" N ASP B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.824A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 4.124A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.940A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 4.323A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 removed outlier: 3.894A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 4.327A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 4.326A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.956A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 578' Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.714A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.131A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 890 removed outlier: 4.251A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 934 Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 978 through 1005 removed outlier: 4.389A pdb=" N THR B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG B1000 " --> pdb=" O TRP B 996 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN B1003 " --> pdb=" O ASP B 999 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1047 removed outlier: 3.525A pdb=" N ASP B1037 " --> pdb=" O ARG B1033 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1212 removed outlier: 3.962A pdb=" N LEU B1211 " --> pdb=" O ASP B1207 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1207 through 1212' Processing helix chain 'B' and resid 1574 through 1581 removed outlier: 4.306A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.174A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG B1656 " --> pdb=" O GLU B1652 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1649 through 1657' Processing helix chain 'B' and resid 1658 through 1675 Processing helix chain 'B' and resid 1678 through 1690 removed outlier: 4.705A pdb=" N ALA B1682 " --> pdb=" O ASN B1678 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B1690 " --> pdb=" O CYS B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1700 removed outlier: 3.941A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 6.838A pdb=" N ARG B1708 " --> pdb=" O PRO B1704 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1732 removed outlier: 4.369A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 4.367A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1759 removed outlier: 4.341A pdb=" N ARG B1759 " --> pdb=" O GLY B1755 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.588A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1865 removed outlier: 3.957A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1984 removed outlier: 3.735A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B1951 " --> pdb=" O CYS B1947 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 2000 removed outlier: 3.945A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER B2000 " --> pdb=" O ARG B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 3.581A pdb=" N LEU B2009 " --> pdb=" O GLN B2005 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B2010 " --> pdb=" O ILE B2006 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2028 through 2043 removed outlier: 3.968A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 4.232A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.620A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2141 Proline residue: B2139 - end of helix Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 4.202A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B2155 " --> pdb=" O ASP B2151 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2188 removed outlier: 3.714A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2195 removed outlier: 5.120A pdb=" N GLN B2193 " --> pdb=" O LYS B2189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B2194 " --> pdb=" O VAL B2190 " (cutoff:3.500A) Proline residue: B2195 - end of helix No H-bonds generated for 'chain 'B' and resid 2189 through 2195' Processing helix chain 'B' and resid 2196 through 2202 Processing helix chain 'B' and resid 2203 through 2216 removed outlier: 4.067A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2244 removed outlier: 4.881A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2254 removed outlier: 4.091A pdb=" N SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2255 through 2265 removed outlier: 3.615A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B2264 " --> pdb=" O ASN B2260 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2283 removed outlier: 4.386A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B2282 " --> pdb=" O ALA B2278 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASN B2283 " --> pdb=" O SER B2279 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 3.760A pdb=" N GLN B2291 " --> pdb=" O ALA B2287 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2309 removed outlier: 3.685A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR B2301 " --> pdb=" O LYS B2297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B2302 " --> pdb=" O VAL B2298 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.748A pdb=" N LEU B2314 " --> pdb=" O CYS B2310 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 4.652A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.959A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2365 through 2370 Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2438 Proline residue: B2438 - end of helix Processing helix chain 'B' and resid 2440 through 2447 Processing helix chain 'B' and resid 2448 through 2462 removed outlier: 3.599A pdb=" N ARG B2452 " --> pdb=" O GLY B2448 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2464 through 2472 removed outlier: 4.576A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 4.680A pdb=" N ILE B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B2762 " --> pdb=" O PHE B2758 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B2764 " --> pdb=" O GLU B2760 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP B2766 " --> pdb=" O THR B2762 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B2767 " --> pdb=" O HIS B2763 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B2770 " --> pdb=" O TRP B2766 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE B2771 " --> pdb=" O ALA B2767 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLN B2772 " --> pdb=" O PHE B2768 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B2773 " --> pdb=" O ASP B2769 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2804 removed outlier: 5.032A pdb=" N LYS B2802 " --> pdb=" O SER B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2873 removed outlier: 5.187A pdb=" N GLN B2872 " --> pdb=" O SER B2868 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA B2873 " --> pdb=" O ARG B2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2868 through 2873' Processing helix chain 'B' and resid 2874 through 2892 removed outlier: 4.328A pdb=" N ALA B2879 " --> pdb=" O ALA B2875 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B2881 " --> pdb=" O GLN B2877 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR B2882 " --> pdb=" O LEU B2878 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B2890 " --> pdb=" O TRP B2886 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS B2891 " --> pdb=" O GLY B2887 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN B2892 " --> pdb=" O ARG B2888 " (cutoff:3.500A) Processing helix chain 'B' and resid 2919 through 2930 removed outlier: 4.716A pdb=" N ALA B2923 " --> pdb=" O ASP B2919 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B2925 " --> pdb=" O GLU B2921 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS B2928 " --> pdb=" O GLN B2924 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B2929 " --> pdb=" O GLU B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3657 removed outlier: 3.943A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER B3656 " --> pdb=" O MET B3652 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR B3657 " --> pdb=" O PHE B3653 " (cutoff:3.500A) Processing helix chain 'B' and resid 3668 through 3681 Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3738 removed outlier: 3.677A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B3738 " --> pdb=" O HIS B3734 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.820A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 4.116A pdb=" N SER B3795 " --> pdb=" O GLY B3791 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3827 through 3839 removed outlier: 4.133A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3857 removed outlier: 4.221A pdb=" N GLY B3857 " --> pdb=" O ALA B3853 " (cutoff:3.500A) Processing helix chain 'B' and resid 3863 through 3870 removed outlier: 3.989A pdb=" N ASN B3867 " --> pdb=" O GLY B3863 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 3.633A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3905 removed outlier: 4.817A pdb=" N LEU B3903 " --> pdb=" O PHE B3899 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B3904 " --> pdb=" O GLN B3900 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 6.317A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B3922 " --> pdb=" O CYS B3918 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.670A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B3968 " --> pdb=" O SER B3964 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 4.930A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4007 removed outlier: 3.957A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER B4007 " --> pdb=" O LEU B4003 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 Processing helix chain 'B' and resid 4038 through 4052 Processing helix chain 'B' and resid 4053 through 4074 Processing helix chain 'B' and resid 4075 through 4082 removed outlier: 5.108A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 4.571A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4124 through 4134 removed outlier: 5.180A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Processing helix chain 'B' and resid 4135 through 4155 removed outlier: 4.429A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 4.453A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 Processing helix chain 'B' and resid 4198 through 4207 removed outlier: 3.888A pdb=" N GLN B4204 " --> pdb=" O THR B4200 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP B4205 " --> pdb=" O ASN B4201 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4541 through 4559 Processing helix chain 'B' and resid 4560 through 4580 removed outlier: 3.805A pdb=" N PHE B4564 " --> pdb=" O TYR B4560 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR B4580 " --> pdb=" O ILE B4576 " (cutoff:3.500A) Processing helix chain 'B' and resid 4642 through 4684 removed outlier: 5.241A pdb=" N LEU B4646 " --> pdb=" O ALA B4642 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix Processing helix chain 'B' and resid 4696 through 4709 removed outlier: 4.208A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B4708 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Proline residue: B4709 - end of helix Processing helix chain 'B' and resid 4719 through 4729 Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 3.598A pdb=" N LEU B4740 " --> pdb=" O ARG B4736 " (cutoff:3.500A) Processing helix chain 'B' and resid 4749 through 4754 Processing helix chain 'B' and resid 4766 through 4771 Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 4.483A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4805 removed outlier: 4.918A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASN B4805 " --> pdb=" O LEU B4801 " (cutoff:3.500A) Processing helix chain 'B' and resid 4809 through 4819 removed outlier: 4.758A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4859 removed outlier: 3.576A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B4834 " --> pdb=" O VAL B4830 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS B4835 " --> pdb=" O THR B4831 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLN B4836 " --> pdb=" O HIS B4832 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B4840 " --> pdb=" O GLN B4836 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.492A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4902 removed outlier: 4.424A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) Processing helix chain 'B' and resid 4910 through 4957 removed outlier: 6.510A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B4926 " --> pdb=" O PHE B4922 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B4927 " --> pdb=" O PHE B4923 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B4928 " --> pdb=" O VAL B4924 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B4929 " --> pdb=" O ILE B4925 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B4957 " --> pdb=" O ASP B4953 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4972 removed outlier: 4.185A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Proline residue: B4972 - end of helix Processing helix chain 'B' and resid 4973 through 4981 removed outlier: 4.585A pdb=" N THR B4979 " --> pdb=" O PHE B4975 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B4980 " --> pdb=" O GLU B4976 " (cutoff:3.500A) Processing helix chain 'B' and resid 4984 through 4998 removed outlier: 3.558A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5027 through 5033 removed outlier: 6.194A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1222 Processing helix chain 'B' and resid 4685 through 4690 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.379A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 249 through 256 removed outlier: 4.378A pdb=" N CYS C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 256' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.960A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 423 removed outlier: 4.078A pdb=" N ASP C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 3.867A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE C 442 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.622A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 4.876A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 532 removed outlier: 4.195A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 540 removed outlier: 4.378A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 4.263A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.353A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 567 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.994A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 578' Processing helix chain 'C' and resid 579 through 594 Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.743A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 4.237A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 4.263A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 934 Processing helix chain 'C' and resid 956 through 961 Processing helix chain 'C' and resid 978 through 1005 removed outlier: 4.381A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG C1000 " --> pdb=" O TRP C 996 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA C1002 " --> pdb=" O ARG C 998 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN C1003 " --> pdb=" O ASP C 999 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1047 removed outlier: 3.524A pdb=" N ASP C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1212 removed outlier: 4.069A pdb=" N LEU C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ARG C1212 " --> pdb=" O VAL C1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1207 through 1212' Processing helix chain 'C' and resid 1574 through 1581 removed outlier: 4.179A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 4.109A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG C1656 " --> pdb=" O GLU C1652 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1649 through 1657' Processing helix chain 'C' and resid 1658 through 1675 Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 4.790A pdb=" N ALA C1682 " --> pdb=" O ASN C1678 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS C1683 " --> pdb=" O ASN C1679 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1700 removed outlier: 3.929A pdb=" N LEU C1698 " --> pdb=" O LEU C1694 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 removed outlier: 6.865A pdb=" N ARG C1708 " --> pdb=" O PRO C1704 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1732 removed outlier: 4.155A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 4.451A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1754 through 1759 removed outlier: 4.337A pdb=" N ARG C1759 " --> pdb=" O GLY C1755 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.653A pdb=" N LEU C1807 " --> pdb=" O PRO C1803 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1865 removed outlier: 3.933A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1935 through 1984 removed outlier: 3.691A pdb=" N TYR C1945 " --> pdb=" O ASN C1941 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C1951 " --> pdb=" O CYS C1947 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C1964 " --> pdb=" O ALA C1960 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 2000 removed outlier: 3.888A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER C2000 " --> pdb=" O ARG C1996 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 3.649A pdb=" N LEU C2009 " --> pdb=" O GLN C2005 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C2010 " --> pdb=" O ILE C2006 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2028 through 2043 removed outlier: 4.036A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 4.373A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.531A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2141 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 4.179A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C2155 " --> pdb=" O ASP C2151 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2188 removed outlier: 3.900A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2195 removed outlier: 5.110A pdb=" N GLN C2193 " --> pdb=" O LYS C2189 " (cutoff:3.500A) Proline residue: C2195 - end of helix Processing helix chain 'C' and resid 2196 through 2202 Processing helix chain 'C' and resid 2203 through 2216 removed outlier: 4.125A pdb=" N VAL C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2227 through 2244 removed outlier: 4.792A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2254 removed outlier: 4.174A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2255 through 2265 removed outlier: 3.664A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2283 removed outlier: 4.368A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASN C2283 " --> pdb=" O SER C2279 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2291 removed outlier: 3.538A pdb=" N GLN C2291 " --> pdb=" O ALA C2287 " (cutoff:3.500A) Processing helix chain 'C' and resid 2294 through 2309 removed outlier: 3.697A pdb=" N VAL C2299 " --> pdb=" O LEU C2295 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR C2301 " --> pdb=" O LYS C2297 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C2302 " --> pdb=" O VAL C2298 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 3.745A pdb=" N LEU C2314 " --> pdb=" O CYS C2310 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 4.736A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.735A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2365 through 2370 Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2438 Proline residue: C2438 - end of helix Processing helix chain 'C' and resid 2440 through 2447 Processing helix chain 'C' and resid 2448 through 2462 removed outlier: 3.605A pdb=" N ARG C2452 " --> pdb=" O GLY C2448 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C2453 " --> pdb=" O GLU C2449 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2464 through 2472 removed outlier: 4.403A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 4.760A pdb=" N ILE C2755 " --> pdb=" O LEU C2751 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR C2762 " --> pdb=" O PHE C2758 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C2764 " --> pdb=" O GLU C2760 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP C2766 " --> pdb=" O THR C2762 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C2767 " --> pdb=" O HIS C2763 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP C2769 " --> pdb=" O LYS C2765 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE C2771 " --> pdb=" O ALA C2767 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN C2772 " --> pdb=" O PHE C2768 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN C2773 " --> pdb=" O ASP C2769 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2804 removed outlier: 5.005A pdb=" N LYS C2802 " --> pdb=" O SER C2798 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2873 removed outlier: 5.842A pdb=" N GLN C2872 " --> pdb=" O SER C2868 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA C2873 " --> pdb=" O ARG C2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2868 through 2873' Processing helix chain 'C' and resid 2874 through 2892 removed outlier: 4.318A pdb=" N ALA C2879 " --> pdb=" O ALA C2875 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C2881 " --> pdb=" O GLN C2877 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C2882 " --> pdb=" O LEU C2878 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C2890 " --> pdb=" O TRP C2886 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C2891 " --> pdb=" O GLY C2887 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN C2892 " --> pdb=" O ARG C2888 " (cutoff:3.500A) Processing helix chain 'C' and resid 2919 through 2930 removed outlier: 4.824A pdb=" N ALA C2923 " --> pdb=" O ASP C2919 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C2925 " --> pdb=" O GLU C2921 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS C2928 " --> pdb=" O GLN C2924 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C2929 " --> pdb=" O GLU C2925 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3657 removed outlier: 3.971A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER C3656 " --> pdb=" O MET C3652 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR C3657 " --> pdb=" O PHE C3653 " (cutoff:3.500A) Processing helix chain 'C' and resid 3668 through 3681 Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3738 removed outlier: 3.663A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU C3736 " --> pdb=" O SER C3732 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C3738 " --> pdb=" O HIS C3734 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.821A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 4.071A pdb=" N SER C3795 " --> pdb=" O GLY C3791 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3827 through 3839 removed outlier: 4.174A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3857 removed outlier: 4.205A pdb=" N GLY C3857 " --> pdb=" O ALA C3853 " (cutoff:3.500A) Processing helix chain 'C' and resid 3863 through 3870 removed outlier: 3.973A pdb=" N ASN C3867 " --> pdb=" O GLY C3863 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3893 removed outlier: 3.658A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3905 removed outlier: 4.848A pdb=" N LEU C3903 " --> pdb=" O PHE C3899 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C3904 " --> pdb=" O GLN C3900 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 6.246A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.642A pdb=" N GLU C3967 " --> pdb=" O ASN C3963 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C3968 " --> pdb=" O SER C3964 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 4.931A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4007 removed outlier: 4.044A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER C4007 " --> pdb=" O LEU C4003 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 Processing helix chain 'C' and resid 4038 through 4052 Processing helix chain 'C' and resid 4053 through 4074 Processing helix chain 'C' and resid 4075 through 4082 removed outlier: 5.109A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 4.782A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4124 through 4134 removed outlier: 5.331A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Processing helix chain 'C' and resid 4135 through 4155 removed outlier: 4.338A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 4.283A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 Processing helix chain 'C' and resid 4198 through 4207 removed outlier: 3.907A pdb=" N GLN C4204 " --> pdb=" O THR C4200 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP C4205 " --> pdb=" O ASN C4201 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C4206 " --> pdb=" O ARG C4202 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4541 through 4559 Processing helix chain 'C' and resid 4560 through 4580 removed outlier: 3.599A pdb=" N PHE C4564 " --> pdb=" O TYR C4560 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TYR C4580 " --> pdb=" O ILE C4576 " (cutoff:3.500A) Processing helix chain 'C' and resid 4642 through 4684 removed outlier: 4.900A pdb=" N LEU C4646 " --> pdb=" O ALA C4642 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix Processing helix chain 'C' and resid 4696 through 4709 removed outlier: 4.324A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR C4708 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Proline residue: C4709 - end of helix Processing helix chain 'C' and resid 4719 through 4729 Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4749 through 4754 Processing helix chain 'C' and resid 4766 through 4771 Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 3.768A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4805 removed outlier: 4.715A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASN C4805 " --> pdb=" O LEU C4801 " (cutoff:3.500A) Processing helix chain 'C' and resid 4809 through 4819 removed outlier: 4.824A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4859 removed outlier: 3.857A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY C4834 " --> pdb=" O VAL C4830 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS C4835 " --> pdb=" O THR C4831 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLN C4836 " --> pdb=" O HIS C4832 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET C4839 " --> pdb=" O LYS C4835 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C4840 " --> pdb=" O GLN C4836 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.727A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4902 removed outlier: 4.397A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) Processing helix chain 'C' and resid 4910 through 4957 removed outlier: 6.544A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C4925 " --> pdb=" O PHE C4921 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C4926 " --> pdb=" O PHE C4922 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C4927 " --> pdb=" O PHE C4923 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C4928 " --> pdb=" O VAL C4924 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C4929 " --> pdb=" O ILE C4925 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C4936 " --> pdb=" O ILE C4932 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4972 removed outlier: 3.954A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C4971 " --> pdb=" O TYR C4967 " (cutoff:3.500A) Proline residue: C4972 - end of helix Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 removed outlier: 6.123A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5027 through 5033 removed outlier: 6.380A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1222 Processing helix chain 'C' and resid 4685 through 4690 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.450A 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 249 through 256 removed outlier: 4.663A pdb=" N CYS D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 256' Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.017A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 423 removed outlier: 4.168A pdb=" N ASP D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 3.868A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE D 442 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 4.029A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 4.978A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.213A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLY D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 540 removed outlier: 3.903A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 551 removed outlier: 4.329A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 4.305A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.074A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 572 through 578' Processing helix chain 'D' and resid 579 through 594 Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.730A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 4.298A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP D 619 " --> pdb=" O ARG D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 890 removed outlier: 4.288A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU D 888 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 934 Processing helix chain 'D' and resid 956 through 961 Processing helix chain 'D' and resid 978 through 1005 removed outlier: 4.364A pdb=" N THR D 982 " --> pdb=" O THR D 978 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG D1000 " --> pdb=" O TRP D 996 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA D1002 " --> pdb=" O ARG D 998 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN D1003 " --> pdb=" O ASP D 999 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY D1004 " --> pdb=" O ARG D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1047 removed outlier: 4.340A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1207 through 1212 removed outlier: 3.976A pdb=" N LEU D1211 " --> pdb=" O ASP D1207 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1207 through 1212' Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 4.179A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.077A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.267A 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 removed outlier: 4.898A pdb=" N ALA D1682 " --> pdb=" O ASN D1678 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP D1690 " --> pdb=" O CYS D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1700 removed outlier: 3.576A pdb=" N LEU D1698 " --> pdb=" O LEU D1694 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 removed outlier: 6.895A pdb=" N ARG D1708 " --> pdb=" O PRO D1704 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D1709 " --> pdb=" O GLY D1705 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS D1719 " --> pdb=" O LEU D1715 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1732 removed outlier: 4.176A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 4.435A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1754 through 1759 removed outlier: 4.357A pdb=" N ARG D1759 " --> pdb=" O GLY D1755 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.672A pdb=" N LEU D1807 " --> pdb=" O PRO D1803 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1865 removed outlier: 3.978A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1935 through 1984 removed outlier: 3.727A pdb=" N TYR D1945 " --> pdb=" O ASN D1941 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D1950 " --> pdb=" O PHE D1946 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D1951 " --> pdb=" O CYS D1947 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D1964 " --> pdb=" O ALA D1960 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 2000 removed outlier: 3.911A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER D2000 " --> pdb=" O ARG D1996 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 3.518A pdb=" N LEU D2009 " --> pdb=" O GLN D2005 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D2010 " --> pdb=" O ILE D2006 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2028 through 2043 removed outlier: 3.890A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 4.268A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.619A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2141 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.232A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D2155 " --> pdb=" O ASP D2151 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2188 removed outlier: 3.653A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2195 removed outlier: 5.072A pdb=" N GLN D2193 " --> pdb=" O LYS D2189 " (cutoff:3.500A) Proline residue: D2195 - end of helix Processing helix chain 'D' and resid 2196 through 2202 Processing helix chain 'D' and resid 2203 through 2216 removed outlier: 4.072A pdb=" N VAL D2214 " --> pdb=" O VAL D2210 " (cutoff:3.500A) Processing helix chain 'D' and resid 2227 through 2244 removed outlier: 4.859A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2254 removed outlier: 4.036A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2255 through 2265 removed outlier: 3.674A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D2264 " --> pdb=" O ASN D2260 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2283 removed outlier: 4.383A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA D2276 " --> pdb=" O PRO D2272 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN D2283 " --> pdb=" O SER D2279 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2291 removed outlier: 3.643A pdb=" N GLN D2291 " --> pdb=" O ALA D2287 " (cutoff:3.500A) Processing helix chain 'D' and resid 2294 through 2309 removed outlier: 3.748A pdb=" N VAL D2299 " --> pdb=" O LEU D2295 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER D2300 " --> pdb=" O GLU D2296 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR D2301 " --> pdb=" O LYS D2297 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU D2302 " --> pdb=" O VAL D2298 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 3.752A pdb=" N LEU D2314 " --> pdb=" O CYS D2310 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 4.825A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.970A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2365 through 2370 Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2438 Proline residue: D2438 - end of helix Processing helix chain 'D' and resid 2440 through 2447 Processing helix chain 'D' and resid 2448 through 2462 removed outlier: 3.618A pdb=" N ARG D2452 " --> pdb=" O GLY D2448 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D2453 " --> pdb=" O GLU D2449 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2464 through 2472 removed outlier: 4.654A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 4.917A pdb=" N ILE D2755 " --> pdb=" O LEU D2751 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR D2762 " --> pdb=" O PHE D2758 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D2764 " --> pdb=" O GLU D2760 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP D2766 " --> pdb=" O THR D2762 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA D2767 " --> pdb=" O HIS D2763 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP D2769 " --> pdb=" O LYS D2765 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS D2770 " --> pdb=" O TRP D2766 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE D2771 " --> pdb=" O ALA D2767 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN D2772 " --> pdb=" O PHE D2768 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN D2773 " --> pdb=" O ASP D2769 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2804 removed outlier: 5.050A pdb=" N LYS D2802 " --> pdb=" O SER D2798 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2873 removed outlier: 5.582A pdb=" N GLN D2872 " --> pdb=" O SER D2868 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA D2873 " --> pdb=" O ARG D2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2868 through 2873' Processing helix chain 'D' and resid 2874 through 2892 removed outlier: 4.266A pdb=" N ALA D2879 " --> pdb=" O ALA D2875 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN D2881 " --> pdb=" O GLN D2877 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR D2882 " --> pdb=" O LEU D2878 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS D2890 " --> pdb=" O TRP D2886 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS D2891 " --> pdb=" O GLY D2887 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLN D2892 " --> pdb=" O ARG D2888 " (cutoff:3.500A) Processing helix chain 'D' and resid 2919 through 2930 removed outlier: 4.854A pdb=" N ALA D2923 " --> pdb=" O ASP D2919 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU D2925 " --> pdb=" O GLU D2921 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS D2928 " --> pdb=" O GLN D2924 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D2929 " --> pdb=" O GLU D2925 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3657 removed outlier: 3.998A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D3656 " --> pdb=" O MET D3652 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR D3657 " --> pdb=" O PHE D3653 " (cutoff:3.500A) Processing helix chain 'D' and resid 3668 through 3681 Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3738 removed outlier: 3.747A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU D3736 " --> pdb=" O SER D3732 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D3738 " --> pdb=" O HIS D3734 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.807A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 4.095A pdb=" N SER D3795 " --> pdb=" O GLY D3791 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3827 through 3839 removed outlier: 4.039A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3857 removed outlier: 4.195A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) Processing helix chain 'D' and resid 3863 through 3870 removed outlier: 3.958A pdb=" N ASN D3867 " --> pdb=" O GLY D3863 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 3.649A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3905 removed outlier: 4.756A pdb=" N LEU D3903 " --> pdb=" O PHE D3899 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D3904 " --> pdb=" O GLN D3900 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 6.385A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D3922 " --> pdb=" O CYS D3918 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.670A pdb=" N GLU D3967 " --> pdb=" O ASN D3963 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D3968 " --> pdb=" O SER D3964 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 5.034A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4007 removed outlier: 3.734A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 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: 5.069A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 4.410A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4124 through 4134 removed outlier: 5.317A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Processing helix chain 'D' and resid 4135 through 4155 removed outlier: 4.306A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 4.403A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 3.894A pdb=" N GLN D4204 " --> pdb=" O THR D4200 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D4205 " --> pdb=" O ASN D4201 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D4206 " --> pdb=" O ARG D4202 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4541 through 4559 Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 3.714A pdb=" N PHE D4564 " --> pdb=" O TYR D4560 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4642 through 4684 removed outlier: 4.898A pdb=" N LEU D4646 " --> pdb=" O ALA D4642 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix Processing helix chain 'D' and resid 4696 through 4709 removed outlier: 4.254A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.007A 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 4729 Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 3.516A pdb=" N LEU D4740 " --> pdb=" O ARG D4736 " (cutoff:3.500A) Processing helix chain 'D' and resid 4749 through 4754 Processing helix chain 'D' and resid 4766 through 4771 Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 3.976A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4805 removed outlier: 4.832A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN D4805 " --> pdb=" O LEU D4801 " (cutoff:3.500A) Processing helix chain 'D' and resid 4809 through 4819 removed outlier: 4.733A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY D4819 " --> pdb=" O ASP D4815 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4859 removed outlier: 3.935A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D4834 " --> pdb=" O VAL D4830 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS D4835 " --> pdb=" O THR D4831 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN D4836 " --> pdb=" O HIS D4832 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET D4839 " --> pdb=" O LYS D4835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR D4840 " --> pdb=" O GLN D4836 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.796A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4902 removed outlier: 4.447A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) Processing helix chain 'D' and resid 4910 through 4957 removed outlier: 6.592A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D4925 " --> pdb=" O PHE D4921 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL D4926 " --> pdb=" O PHE D4922 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D4927 " --> pdb=" O PHE D4923 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU D4928 " --> pdb=" O VAL D4924 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D4929 " --> pdb=" O ILE D4925 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4972 removed outlier: 3.918A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR D4971 " --> pdb=" O TYR D4967 " (cutoff:3.500A) Proline residue: D4972 - end of helix Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 removed outlier: 6.532A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 removed outlier: 6.532A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1217 through 1222 Processing helix chain 'D' and resid 4685 through 4690 Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.354A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.965A pdb=" N CYS A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 256' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.928A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.904A pdb=" N ASP A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.213A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 4.012A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.889A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.391A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 4.283A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.317A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.023A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.279A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 578' Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.750A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 removed outlier: 4.410A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 4.075A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 934 Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 978 through 1005 removed outlier: 4.251A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A1000 " --> pdb=" O TRP A 996 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 removed outlier: 3.857A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1212 removed outlier: 3.868A pdb=" N LEU A1211 " --> pdb=" O ASP A1207 " (cutoff:3.500A) removed outlier: 5.502A 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 1574 through 1581 removed outlier: 3.750A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1574 through 1581' Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.168A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.377A 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: 4.769A pdb=" N ALA A1682 " --> pdb=" O ASN A1678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1700 removed outlier: 3.811A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 removed outlier: 6.819A pdb=" N ARG A1708 " --> pdb=" O PRO A1704 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1732 removed outlier: 4.373A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 4.490A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1759 removed outlier: 4.310A pdb=" N ARG A1759 " --> pdb=" O GLY A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.556A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1865 removed outlier: 3.921A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1984 removed outlier: 3.955A pdb=" N TYR A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A1946 " --> pdb=" O LEU A1942 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A1950 " --> pdb=" O PHE A1946 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1951 " --> pdb=" O CYS A1947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A1964 " --> pdb=" O ALA A1960 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2000 removed outlier: 3.627A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A2000 " --> pdb=" O ARG A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 3.633A pdb=" N LEU A2009 " --> pdb=" O GLN A2005 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2043 removed outlier: 4.095A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 4.051A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.700A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.123A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A2155 " --> pdb=" O ASP A2151 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2188 removed outlier: 3.844A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2195 removed outlier: 5.419A pdb=" N GLN A2193 " --> pdb=" O LYS A2189 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS A2194 " --> pdb=" O VAL A2190 " (cutoff:3.500A) Proline residue: A2195 - end of helix No H-bonds generated for 'chain 'A' and resid 2189 through 2195' Processing helix chain 'A' and resid 2196 through 2202 Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 3.973A pdb=" N VAL A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2244 removed outlier: 4.875A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2254 removed outlier: 4.091A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2255 through 2265 removed outlier: 3.588A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A2264 " --> pdb=" O ASN A2260 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2283 removed outlier: 4.419A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASN A2283 " --> pdb=" O SER A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 3.812A pdb=" N GLN A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2309 removed outlier: 3.741A pdb=" N VAL A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER A2300 " --> pdb=" O GLU A2296 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A2301 " --> pdb=" O LYS A2297 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 4.800A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.780A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2365 through 2370 Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2438 Proline residue: A2438 - end of helix Processing helix chain 'A' and resid 2440 through 2447 Processing helix chain 'A' and resid 2448 through 2462 removed outlier: 4.177A pdb=" N ARG A2452 " --> pdb=" O GLY A2448 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A2453 " --> pdb=" O GLU A2449 " (cutoff:3.500A) Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2464 through 2472 removed outlier: 4.693A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 4.849A pdb=" N ILE A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A2764 " --> pdb=" O GLU A2760 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A2766 " --> pdb=" O THR A2762 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A2767 " --> pdb=" O HIS A2763 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP A2769 " --> pdb=" O LYS A2765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A2771 " --> pdb=" O ALA A2767 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLN A2772 " --> pdb=" O PHE A2768 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A2773 " --> pdb=" O ASP A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2804 removed outlier: 5.037A pdb=" N LYS A2802 " --> pdb=" O SER A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2873 removed outlier: 5.471A pdb=" N GLN A2872 " --> pdb=" O SER A2868 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA A2873 " --> pdb=" O ARG A2869 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2868 through 2873' Processing helix chain 'A' and resid 2874 through 2892 removed outlier: 4.494A pdb=" N ALA A2879 " --> pdb=" O ALA A2875 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A2881 " --> pdb=" O GLN A2877 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A2882 " --> pdb=" O LEU A2878 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A2890 " --> pdb=" O TRP A2886 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A2891 " --> pdb=" O GLY A2887 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A2892 " --> pdb=" O ARG A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2930 removed outlier: 4.551A pdb=" N ALA A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A2925 " --> pdb=" O GLU A2921 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS A2928 " --> pdb=" O GLN A2924 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A2929 " --> pdb=" O GLU A2925 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3657 removed outlier: 4.550A pdb=" N SER A3656 " --> pdb=" O MET A3652 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3681 Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3738 removed outlier: 3.674A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A3736 " --> pdb=" O SER A3732 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A3737 " --> pdb=" O CYS A3733 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A3738 " --> pdb=" O HIS A3734 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.563A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.900A pdb=" N SER A3795 " --> pdb=" O GLY A3791 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3827 through 3839 removed outlier: 4.538A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3857 removed outlier: 4.244A pdb=" N GLY A3857 " --> pdb=" O ALA A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3870 removed outlier: 3.966A pdb=" N ASN A3867 " --> pdb=" O GLY A3863 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.685A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3905 removed outlier: 4.839A pdb=" N LEU A3903 " --> pdb=" O PHE A3899 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A3904 " --> pdb=" O GLN A3900 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 6.017A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A3922 " --> pdb=" O CYS A3918 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.508A pdb=" N GLU A3967 " --> pdb=" O ASN A3963 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 5.025A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4007 removed outlier: 3.610A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 5.079A 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 Processing helix chain 'A' and resid 4053 through 4074 Processing helix chain 'A' and resid 4075 through 4082 removed outlier: 5.141A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 3.545A pdb=" N LYS A4095 " --> pdb=" O LYS A4091 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4124 through 4134 removed outlier: 5.583A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4155 removed outlier: 4.486A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A4140 " --> pdb=" O ALA A4136 " (cutoff:3.500A) Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 4.360A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 3.871A pdb=" N GLN A4204 " --> pdb=" O THR A4200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A4205 " --> pdb=" O ASN A4201 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A4206 " --> pdb=" O ARG A4202 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4541 through 4559 Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 3.800A pdb=" N PHE A4564 " --> pdb=" O TYR A4560 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4684 removed outlier: 4.987A pdb=" N LEU A4646 " --> pdb=" O ALA A4642 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.316A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.089A 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 4729 Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 3.586A pdb=" N LEU A4740 " --> pdb=" O ARG A4736 " (cutoff:3.500A) Processing helix chain 'A' and resid 4749 through 4754 Processing helix chain 'A' and resid 4766 through 4771 Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 4.088A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4805 removed outlier: 4.789A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN A4805 " --> pdb=" O LEU A4801 " (cutoff:3.500A) Processing helix chain 'A' and resid 4809 through 4819 removed outlier: 4.623A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4859 removed outlier: 3.558A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS A4835 " --> pdb=" O THR A4831 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN A4836 " --> pdb=" O HIS A4832 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N MET A4839 " --> pdb=" O LYS A4835 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A4840 " --> pdb=" O GLN A4836 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.444A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4902 removed outlier: 5.132A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4910 through 4957 removed outlier: 6.606A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A4925 " --> pdb=" O PHE A4921 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL A4926 " --> pdb=" O PHE A4922 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A4927 " --> pdb=" O PHE A4923 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A4928 " --> pdb=" O VAL A4924 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A4929 " --> pdb=" O ILE A4925 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4972 removed outlier: 4.444A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A4971 " --> pdb=" O TYR A4967 " (cutoff:3.500A) Proline residue: A4972 - end of helix Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 removed outlier: 6.017A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 removed outlier: 6.250A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1222 Processing helix chain 'A' and resid 4685 through 4690 Processing sheet with id= 1, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.166A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 12.935A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= 3, first strand: chain 'B' and resid 148 through 153 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= 5, first strand: chain 'B' and resid 230 through 233 removed outlier: 3.690A pdb=" N CYS B 230 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 260 through 264 Processing sheet with id= 7, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= 8, first strand: chain 'B' and resid 681 through 686 Processing sheet with id= 9, first strand: chain 'B' and resid 753 through 759 removed outlier: 3.715A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 669 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP B1626 " --> pdb=" O PHE B 791 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 829 through 833 removed outlier: 5.049A pdb=" N TYR B 829 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 937 through 940 removed outlier: 4.349A pdb=" N GLY B1050 " --> pdb=" O GLY B 940 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 1122 through 1125 removed outlier: 5.005A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 1129 through 1132 removed outlier: 5.254A pdb=" N GLY B1129 " --> pdb=" O PHE B1139 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B1137 " --> pdb=" O ARG B1131 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 1243 through 1247 Processing sheet with id= 15, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 7.605A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.207A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU C 33 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.103A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 116 through 120 Processing sheet with id= 18, first strand: chain 'C' and resid 148 through 153 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'C' and resid 181 through 184 Processing sheet with id= 20, first strand: chain 'C' and resid 230 through 233 Processing sheet with id= 21, first strand: chain 'C' and resid 260 through 264 Processing sheet with id= 22, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= 23, first strand: chain 'C' and resid 681 through 686 Processing sheet with id= 24, first strand: chain 'C' and resid 753 through 759 removed outlier: 3.700A pdb=" N GLU C 665 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 669 " --> pdb=" O LYS C 788 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP C1626 " --> pdb=" O PHE C 791 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 829 through 833 removed outlier: 5.101A pdb=" N TYR C 829 " --> pdb=" O VAL C 840 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY C 836 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 937 through 940 removed outlier: 3.520A pdb=" N GLY C 940 " --> pdb=" O GLY C1050 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY C1050 " --> pdb=" O GLY C 940 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 1122 through 1125 removed outlier: 5.003A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 1129 through 1132 removed outlier: 5.236A pdb=" N GLY C1129 " --> pdb=" O PHE C1139 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C1137 " --> pdb=" O ARG C1131 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 1243 through 1247 Processing sheet with id= 30, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 7.606A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.194A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 33 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 12.978A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= 33, first strand: chain 'D' and resid 148 through 153 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'D' and resid 181 through 184 Processing sheet with id= 35, first strand: chain 'D' and resid 230 through 233 removed outlier: 3.735A pdb=" N CYS D 230 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 260 through 264 Processing sheet with id= 37, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= 38, first strand: chain 'D' and resid 681 through 686 Processing sheet with id= 39, first strand: chain 'D' and resid 753 through 759 removed outlier: 3.726A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP D 669 " --> pdb=" O LYS D 788 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TRP D1626 " --> pdb=" O PHE D 791 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 829 through 833 removed outlier: 5.070A pdb=" N TYR D 829 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY D 836 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 937 through 940 removed outlier: 4.394A pdb=" N GLY D1050 " --> pdb=" O GLY D 940 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 1122 through 1125 removed outlier: 4.988A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 1129 through 1132 removed outlier: 5.194A pdb=" N GLY D1129 " --> pdb=" O PHE D1139 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D1137 " --> pdb=" O ARG D1131 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 1243 through 1247 Processing sheet with id= 45, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 7.638A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.448A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 33 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 12.861A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= 48, first strand: chain 'A' and resid 148 through 153 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'A' and resid 181 through 184 Processing sheet with id= 50, first strand: chain 'A' and resid 230 through 233 Processing sheet with id= 51, first strand: chain 'A' and resid 260 through 264 Processing sheet with id= 52, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 53, first strand: chain 'A' and resid 681 through 686 Processing sheet with id= 54, first strand: chain 'A' and resid 753 through 759 removed outlier: 3.777A pdb=" N GLU A 665 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 669 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP A1626 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'A' and resid 829 through 833 removed outlier: 4.975A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY A 836 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'A' and resid 937 through 940 removed outlier: 3.827A pdb=" N GLY A 940 " --> pdb=" O GLY A1050 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY A1050 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'A' and resid 1122 through 1125 removed outlier: 5.033A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'A' and resid 1129 through 1132 removed outlier: 5.263A pdb=" N GLY A1129 " --> pdb=" O PHE A1139 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A1137 " --> pdb=" O ARG A1131 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'A' and resid 1243 through 1247 Processing sheet with id= 60, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 8.039A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) 4563 hydrogen bonds defined for protein. 13599 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: 59.02 Time building geometry restraints manager: 37.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.15: 1 1.15 - 1.33: 22161 1.33 - 1.51: 48276 1.51 - 1.68: 47858 1.68 - 1.86: 1004 Bond restraints: 119300 Sorted by residual: bond pdb=" CG PRO D4709 " pdb=" CD PRO D4709 " ideal model delta sigma weight residual 1.503 0.971 0.532 3.40e-02 8.65e+02 2.45e+02 bond pdb=" C1' ACP B5101 " pdb=" O4' ACP B5101 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ACP D5101 " pdb=" O4' ACP D5101 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ACP C5101 " pdb=" O4' ACP C5101 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ACP A5101 " pdb=" O4' ACP A5101 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 119295 not shown) Histogram of bond angle deviations from ideal: 79.83 - 91.18: 2 91.18 - 102.53: 443 102.53 - 113.88: 68898 113.88 - 125.23: 91461 125.23 - 136.58: 1884 Bond angle restraints: 162688 Sorted by residual: angle pdb=" N PRO D4709 " pdb=" CD PRO D4709 " pdb=" CG PRO D4709 " ideal model delta sigma weight residual 103.20 79.83 23.37 1.50e+00 4.44e-01 2.43e+02 angle pdb=" CA PRO D4709 " pdb=" N PRO D4709 " pdb=" CD PRO D4709 " ideal model delta sigma weight residual 112.00 96.65 15.35 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO A2462 " pdb=" N PRO A2462 " pdb=" CD PRO A2462 " ideal model delta sigma weight residual 112.00 97.50 14.50 1.40e+00 5.10e-01 1.07e+02 angle pdb=" CA PRO B 967 " pdb=" N PRO B 967 " pdb=" CD PRO B 967 " ideal model delta sigma weight residual 112.00 97.80 14.20 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO C 967 " pdb=" N PRO C 967 " pdb=" CD PRO C 967 " ideal model delta sigma weight residual 112.00 98.20 13.80 1.40e+00 5.10e-01 9.71e+01 ... (remaining 162683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 62747 18.01 - 36.01: 6455 36.01 - 54.02: 1665 54.02 - 72.02: 247 72.02 - 90.03: 118 Dihedral angle restraints: 71232 sinusoidal: 23032 harmonic: 48200 Sorted by residual: dihedral pdb=" CA SER A 751 " pdb=" C SER A 751 " pdb=" N VAL A 752 " pdb=" CA VAL A 752 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA TRP C3661 " pdb=" C TRP C3661 " pdb=" N ILE C3662 " pdb=" CA ILE C3662 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TRP D3661 " pdb=" C TRP D3661 " pdb=" N ILE D3662 " pdb=" CA ILE D3662 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 71229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 17616 0.072 - 0.145: 1365 0.145 - 0.217: 44 0.217 - 0.290: 2 0.290 - 0.362: 5 Chirality restraints: 19032 Sorted by residual: chirality pdb=" C2' ACP D5101 " pdb=" C1' ACP D5101 " pdb=" C3' ACP D5101 " pdb=" O2' ACP D5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C2' ACP A5101 " pdb=" C1' ACP A5101 " pdb=" C3' ACP A5101 " pdb=" O2' ACP A5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C2' ACP C5101 " pdb=" C1' ACP C5101 " pdb=" C3' ACP C5101 " pdb=" O2' ACP C5101 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 19029 not shown) Planarity restraints: 21412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.119 5.00e-02 4.00e+02 1.71e-01 4.66e+01 pdb=" N PRO B3972 " -0.295 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.095 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A2461 " 0.121 5.00e-02 4.00e+02 1.70e-01 4.64e+01 pdb=" N PRO A2462 " -0.294 5.00e-02 4.00e+02 pdb=" CA PRO A2462 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO A2462 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 966 " -0.118 5.00e-02 4.00e+02 1.67e-01 4.47e+01 pdb=" N PRO B 967 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO B 967 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO B 967 " -0.082 5.00e-02 4.00e+02 ... (remaining 21409 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3541 2.71 - 3.26: 107764 3.26 - 3.80: 176301 3.80 - 4.35: 197822 4.35 - 4.90: 338531 Nonbonded interactions: 823959 Sorted by model distance: nonbonded pdb=" SG CYS A4961 " pdb=" CG2 ILE A4963 " model vdw 2.159 3.820 nonbonded pdb=" O SER D3768 " pdb=" OG1 THR D3772 " model vdw 2.214 2.440 nonbonded pdb=" O LEU A4837 " pdb=" OG1 THR A4840 " model vdw 2.227 2.440 nonbonded pdb=" O SER A3768 " pdb=" OG1 THR A3772 " model vdw 2.254 2.440 nonbonded pdb=" O LYS D4821 " pdb=" OG1 THR D4825 " model vdw 2.274 2.440 ... (remaining 823954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.110 Extract box with map and model: 22.990 Check model and map are aligned: 1.290 Set scattering table: 0.760 Process input model: 254.220 Find NCS groups from input model: 6.030 Set up NCS constraints: 0.540 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 291.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 0.005 0.532 119300 Z= 0.277 Angle : 0.811 23.373 162688 Z= 0.422 Chirality : 0.038 0.362 19032 Planarity : 0.006 0.171 21412 Dihedral : 16.225 90.027 39860 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.46 % Rotamer Outliers : 0.85 % 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: -0.18 (0.07), residues: 12808 helix: 1.04 (0.06), residues: 6024 sheet: 0.47 (0.17), residues: 964 loop : -1.49 (0.07), residues: 5820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1175 time to evaluate : 9.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 20 residues processed: 1222 average time/residue: 0.9116 time to fit residues: 2008.6194 Evaluate side-chains 1084 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1064 time to evaluate : 9.138 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.8236 time to fit residues: 43.1045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 105 HIS B 151 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 273 HIS ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS B 405 HIS B 460 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 ASN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1274 HIS ** B1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1665 HIS B1683 HIS B1693 GLN B1952 GLN B2095 GLN ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2260 ASN B2420 HIS ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3833 GLN B3895 HIS ** B3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4153 HIS B4209 GLN B4700 GLN ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4776 GLN B4812 HIS B4832 HIS B4886 HIS B4997 ASN C 98 HIS C 105 HIS C 151 HIS C 201 ASN C 273 HIS C 278 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS C 405 HIS C 460 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 597 HIS ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 HIS ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 ASN ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1683 HIS C1693 GLN C1952 GLN C2095 GLN ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2253 HIS C2260 ASN C2420 HIS C2774 ASN ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3647 HIS ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3895 HIS ** C3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4153 HIS C4209 GLN C4650 HIS C4700 GLN ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4776 GLN C4812 HIS ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN D 98 HIS D 105 HIS D 151 HIS ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN D 278 GLN D 380 GLN D 383 HIS D 405 HIS ** D 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 HIS D 909 ASN ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1035 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1201 HIS ** D1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1231 GLN D1254 HIS D1274 HIS D1645 ASN D1683 HIS D1693 GLN D1952 GLN ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2127 GLN D2420 HIS D2774 ASN ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3833 GLN D3895 HIS ** D3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4043 GLN ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4153 HIS D4209 GLN D4650 HIS D4700 GLN D4714 ASN ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4812 HIS D4832 HIS D4997 ASN A 44 ASN A 151 HIS ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 308 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 HIS A 921 ASN ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 GLN A1254 HIS A1274 HIS A1665 HIS A1693 GLN ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2420 HIS A2756 ASN A3647 HIS ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4223 ASN A4650 HIS A4700 GLN ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4812 HIS A4832 HIS A4886 HIS A4997 ASN A5006 GLN A5035 GLN Total number of N/Q/H flips: 121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.9122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.061 0.496 119300 Z= 3.922 Angle : 3.458 35.486 162688 Z= 1.745 Chirality : 0.167 0.919 19032 Planarity : 0.021 0.283 21412 Dihedral : 11.413 65.140 17504 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 62.57 Ramachandran Plot: Outliers : 3.09 % Allowed : 15.28 % Favored : 81.63 % Rotamer Outliers : 17.77 % Cbeta Deviations : 1.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.93 % Twisted General : 1.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.06), residues: 12808 helix: -3.15 (0.05), residues: 5900 sheet: -2.85 (0.14), residues: 1160 loop : -3.96 (0.06), residues: 5748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2512 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1786 poor density : 726 time to evaluate : 9.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1786 outliers final: 1029 residues processed: 2328 average time/residue: 0.9053 time to fit residues: 3802.8417 Evaluate side-chains 1692 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1029 poor density : 663 time to evaluate : 8.412 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1029 outliers final: 7 residues processed: 1029 average time/residue: 0.7949 time to fit residues: 1555.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 113 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 308 HIS ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1274 HIS B1645 ASN B1972 ASN ** B2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2253 HIS B2774 ASN ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3900 GLN ** B3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3909 ASN ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3960 GLN ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4650 HIS ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1274 HIS D1645 ASN ** D2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2184 ASN ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3900 GLN ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3960 GLN D4650 HIS ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4776 GLN ** D4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 113 HIS ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 ASN ** A2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2107 GLN A2253 HIS ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2774 ASN ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN ** A3850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4650 HIS ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4946 GLN ** A4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 1.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.424 119300 Z= 3.882 Angle : 3.360 36.551 162688 Z= 1.692 Chirality : 0.166 0.938 19032 Planarity : 0.021 0.274 21412 Dihedral : 12.658 81.666 17504 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 72.24 Ramachandran Plot: Outliers : 3.15 % Allowed : 24.85 % Favored : 72.00 % Rotamer Outliers : 20.75 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.09 % Twisted General : 2.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.44 (0.05), residues: 12808 helix: -3.93 (0.04), residues: 5908 sheet: -3.56 (0.13), residues: 1112 loop : -4.81 (0.06), residues: 5788 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2692 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2086 poor density : 606 time to evaluate : 9.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2086 outliers final: 1262 residues processed: 2560 average time/residue: 0.9298 time to fit residues: 4252.0801 Evaluate side-chains 1878 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1262 poor density : 616 time to evaluate : 8.336 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 1262 outliers final: 21 residues processed: 1262 average time/residue: 0.8346 time to fit residues: 1994.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4142 ASN ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4984 ASN C 57 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2763 HIS ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2877 GLN ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4120 ASN C4142 ASN ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN D1972 ASN ** D2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2763 HIS ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4130 ASN D4142 ASN ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 1.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.399 119300 Z= 3.891 Angle : 3.368 38.050 162688 Z= 1.695 Chirality : 0.166 0.988 19032 Planarity : 0.021 0.204 21412 Dihedral : 13.124 104.180 17504 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 75.50 Ramachandran Plot: Outliers : 2.44 % Allowed : 29.11 % Favored : 68.44 % Rotamer Outliers : 20.31 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.22 % Twisted General : 2.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.73 (0.05), residues: 12808 helix: -4.08 (0.04), residues: 5796 sheet: -3.96 (0.13), residues: 1112 loop : -5.02 (0.05), residues: 5900 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2619 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2042 poor density : 577 time to evaluate : 9.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2042 outliers final: 1248 residues processed: 2496 average time/residue: 0.9307 time to fit residues: 4154.7468 Evaluate side-chains 1860 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1248 poor density : 612 time to evaluate : 9.412 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1248 outliers final: 33 residues processed: 1248 average time/residue: 0.8532 time to fit residues: 2011.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 ASN ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS B 963 ASN ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN B2035 HIS ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4034 ASN B4043 GLN ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 HIS ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2188 ASN ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2877 GLN ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4153 HIS ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 GLN ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS D 963 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4130 ASN ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4833 ASN ** D4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2193 GLN ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 1.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.398 119300 Z= 3.889 Angle : 3.358 32.397 162688 Z= 1.689 Chirality : 0.166 0.974 19032 Planarity : 0.020 0.213 21412 Dihedral : 13.437 96.757 17504 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 77.05 Ramachandran Plot: Outliers : 2.37 % Allowed : 31.43 % Favored : 66.20 % Rotamer Outliers : 17.82 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.72 % Twisted General : 3.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.85 (0.05), residues: 12808 helix: -4.14 (0.04), residues: 5784 sheet: -4.07 (0.13), residues: 1048 loop : -5.12 (0.05), residues: 5976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2373 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1791 poor density : 582 time to evaluate : 9.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1791 outliers final: 1119 residues processed: 2270 average time/residue: 0.9397 time to fit residues: 3807.6942 Evaluate side-chains 1711 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1119 poor density : 592 time to evaluate : 8.442 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1119 outliers final: 37 residues processed: 1119 average time/residue: 0.8888 time to fit residues: 1872.9417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN B1949 GLN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2193 GLN ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2763 HIS ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4833 ASN ** B4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 ASN C 797 HIS ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2877 GLN ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3895 HIS ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4803 HIS ** C4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4833 ASN ** C4984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 HIS D 963 ASN ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2035 HIS A2107 GLN ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4120 ASN A4130 ASN ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 1.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.408 119300 Z= 3.894 Angle : 3.370 32.887 162688 Z= 1.695 Chirality : 0.167 0.958 19032 Planarity : 0.021 0.225 21412 Dihedral : 13.703 102.403 17504 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 77.98 Ramachandran Plot: Outliers : 2.40 % Allowed : 32.55 % Favored : 65.05 % Rotamer Outliers : 14.86 % Cbeta Deviations : 1.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.06 % Twisted General : 3.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.92 (0.05), residues: 12808 helix: -4.16 (0.04), residues: 5760 sheet: -4.15 (0.13), residues: 1048 loop : -5.19 (0.05), residues: 6000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2069 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1494 poor density : 575 time to evaluate : 9.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1494 outliers final: 885 residues processed: 1980 average time/residue: 0.9830 time to fit residues: 3512.7155 Evaluate side-chains 1468 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 885 poor density : 583 time to evaluate : 9.273 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 885 outliers final: 35 residues processed: 885 average time/residue: 0.8538 time to fit residues: 1441.5048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 4.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4153 HIS ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 772 ASN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2877 GLN ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4803 HIS C4812 HIS ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2763 HIS ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 1.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.418 119300 Z= 3.899 Angle : 3.375 32.622 162688 Z= 1.697 Chirality : 0.168 1.127 19032 Planarity : 0.021 0.262 21412 Dihedral : 13.838 103.899 17504 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 78.46 Ramachandran Plot: Outliers : 2.44 % Allowed : 32.98 % Favored : 64.58 % Rotamer Outliers : 12.13 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.06 % Twisted General : 3.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.98 (0.05), residues: 12808 helix: -4.20 (0.04), residues: 5804 sheet: -4.22 (0.13), residues: 1040 loop : -5.23 (0.05), residues: 5964 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1779 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1219 poor density : 560 time to evaluate : 9.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1219 outliers final: 697 residues processed: 1708 average time/residue: 0.9616 time to fit residues: 2930.1543 Evaluate side-chains 1271 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 697 poor density : 574 time to evaluate : 9.504 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 697 outliers final: 33 residues processed: 697 average time/residue: 0.8357 time to fit residues: 1106.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2187 ASN ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 624 ASN ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 772 ASN ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5003 HIS ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4806 ASN ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 1.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.408 119300 Z= 3.903 Angle : 3.376 33.555 162688 Z= 1.699 Chirality : 0.168 0.910 19032 Planarity : 0.021 0.264 21412 Dihedral : 13.909 104.151 17504 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 78.29 Ramachandran Plot: Outliers : 2.28 % Allowed : 33.53 % Favored : 64.19 % Rotamer Outliers : 9.04 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.06 % Twisted General : 3.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.01 (0.05), residues: 12808 helix: -4.22 (0.04), residues: 5852 sheet: -4.29 (0.12), residues: 1088 loop : -5.25 (0.06), residues: 5868 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 909 poor density : 559 time to evaluate : 9.447 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 outliers start: 909 outliers final: 492 residues processed: 1419 average time/residue: 0.9866 time to fit residues: 2513.3049 Evaluate side-chains 1054 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 492 poor density : 562 time to evaluate : 9.385 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 492 outliers final: 35 residues processed: 492 average time/residue: 0.8545 time to fit residues: 807.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4130 ASN D4153 HIS ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2253 HIS ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4806 ASN ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 1.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.417 119300 Z= 3.907 Angle : 3.384 32.223 162688 Z= 1.702 Chirality : 0.169 1.179 19032 Planarity : 0.021 0.269 21412 Dihedral : 13.958 105.997 17504 Min Nonbonded Distance : 1.483 Molprobity Statistics. All-atom Clashscore : 78.69 Ramachandran Plot: Outliers : 2.30 % Allowed : 33.79 % Favored : 63.91 % Rotamer Outliers : 5.95 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.89 % Twisted General : 3.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.03 (0.05), residues: 12808 helix: -4.25 (0.04), residues: 5852 sheet: -4.23 (0.13), residues: 1004 loop : -5.26 (0.06), residues: 5952 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 598 poor density : 554 time to evaluate : 9.796 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 outliers start: 598 outliers final: 316 residues processed: 1110 average time/residue: 0.9858 time to fit residues: 1942.3078 Evaluate side-chains 872 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 556 time to evaluate : 9.376 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 316 outliers final: 35 residues processed: 316 average time/residue: 0.8277 time to fit residues: 500.7235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3895 HIS ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 772 ASN ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 1.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.418 119300 Z= 3.911 Angle : 3.388 35.892 162688 Z= 1.704 Chirality : 0.169 1.520 19032 Planarity : 0.021 0.288 21412 Dihedral : 14.027 107.982 17504 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 78.97 Ramachandran Plot: Outliers : 2.29 % Allowed : 33.91 % Favored : 63.80 % Rotamer Outliers : 3.61 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.06 % Twisted General : 3.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.04 (0.05), residues: 12808 helix: -4.26 (0.04), residues: 5864 sheet: -4.20 (0.13), residues: 1004 loop : -5.27 (0.05), residues: 5940 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 552 time to evaluate : 9.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 363 outliers final: 193 residues processed: 883 average time/residue: 1.0027 time to fit residues: 1599.7998 Evaluate side-chains 737 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 544 time to evaluate : 9.480 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 193 outliers final: 34 residues processed: 193 average time/residue: 0.9005 time to fit residues: 340.9051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 ASN ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 HIS ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3895 HIS ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4803 HIS ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.076232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055435 restraints weight = 466467.022| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.22 r_work: 0.2809 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.415 119300 Z= 3.910 Angle : 3.386 34.088 162688 Z= 1.703 Chirality : 0.169 1.368 19032 Planarity : 0.021 0.285 21412 Dihedral : 14.062 107.549 17504 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 78.91 Ramachandran Plot: Outliers : 2.33 % Allowed : 33.83 % Favored : 63.84 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.39 % Twisted General : 3.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.06 (0.05), residues: 12808 helix: -4.26 (0.04), residues: 5860 sheet: -4.21 (0.13), residues: 1004 loop : -5.29 (0.05), residues: 5944 =============================================================================== Job complete usr+sys time: 70541.75 seconds wall clock time: 1207 minutes 35.77 seconds (72455.77 seconds total)