Starting phenix.real_space_refine (version: dev) on Tue Feb 21 14:41:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/02_2023/6hs7_0264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/02_2023/6hs7_0264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/02_2023/6hs7_0264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/02_2023/6hs7_0264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/02_2023/6hs7_0264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/02_2023/6hs7_0264.pdb" } resolution = 4.6 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 Process input model Symmetric amino acids flipped Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 673": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 727": "NH1" <-> "NH2" Residue "A PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1083": "NH1" <-> "NH2" Residue "B PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 673": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B ARG 727": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1083": "NH1" <-> "NH2" Residue "C PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C ARG 673": "NH1" <-> "NH2" Residue "C ARG 692": "NH1" <-> "NH2" Residue "C ARG 727": "NH1" <-> "NH2" Residue "C PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1083": "NH1" <-> "NH2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D ARG 673": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D ARG 727": "NH1" <-> "NH2" Residue "D PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1083": "NH1" <-> "NH2" Residue "E PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E ARG 673": "NH1" <-> "NH2" Residue "E ARG 692": "NH1" <-> "NH2" Residue "E ARG 727": "NH1" <-> "NH2" Residue "E PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1083": "NH1" <-> "NH2" Residue "a ARG 624": "NH1" <-> "NH2" Residue "a ARG 727": "NH1" <-> "NH2" Residue "a ARG 760": "NH1" <-> "NH2" Residue "a ARG 801": "NH1" <-> "NH2" Residue "a ARG 880": "NH1" <-> "NH2" Residue "a ARG 894": "NH1" <-> "NH2" Residue "a ARG 1097": "NH1" <-> "NH2" Residue "b ARG 624": "NH1" <-> "NH2" Residue "b ARG 727": "NH1" <-> "NH2" Residue "b ARG 760": "NH1" <-> "NH2" Residue "b ARG 801": "NH1" <-> "NH2" Residue "b ARG 880": "NH1" <-> "NH2" Residue "b ARG 894": "NH1" <-> "NH2" Residue "b PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 1097": "NH1" <-> "NH2" Residue "c ARG 624": "NH1" <-> "NH2" Residue "c ARG 727": "NH1" <-> "NH2" Residue "c ARG 760": "NH1" <-> "NH2" Residue "c ARG 801": "NH1" <-> "NH2" Residue "c ARG 880": "NH1" <-> "NH2" Residue "c ARG 894": "NH1" <-> "NH2" Residue "c PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 1097": "NH1" <-> "NH2" Residue "d ARG 624": "NH1" <-> "NH2" Residue "d ARG 727": "NH1" <-> "NH2" Residue "d ARG 760": "NH1" <-> "NH2" Residue "d ARG 801": "NH1" <-> "NH2" Residue "d ARG 880": "NH1" <-> "NH2" Residue "d ARG 894": "NH1" <-> "NH2" Residue "d ARG 1097": "NH1" <-> "NH2" Residue "e ARG 624": "NH1" <-> "NH2" Residue "e ARG 727": "NH1" <-> "NH2" Residue "e ARG 760": "NH1" <-> "NH2" Residue "e ARG 801": "NH1" <-> "NH2" Residue "e ARG 880": "NH1" <-> "NH2" Residue "e ARG 894": "NH1" <-> "NH2" Residue "e PHE 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 1097": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 52890 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "E" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "F" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "b" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "c" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "d" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "e" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 21.30, per 1000 atoms: 0.40 Number of scatterers: 52890 At special positions: 0 Unit cell: (181.04, 182.28, 177.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 170 16.00 O 10045 8.00 N 9330 7.00 C 33345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.50 Conformation dependent library (CDL) restraints added in 6.0 seconds 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12840 Finding SS restraints... Secondary structure from input PDB file: 250 helices and 63 sheets defined 37.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 578 through 589 removed outlier: 4.206A pdb=" N LEU A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 removed outlier: 3.995A pdb=" N ASP A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.569A pdb=" N GLN A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.555A pdb=" N ASN A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.669A pdb=" N THR A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.994A pdb=" N GLN A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.796A pdb=" N THR A 793 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 795 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 removed outlier: 4.577A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 821 " --> pdb=" O MET A 817 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 842 removed outlier: 4.053A pdb=" N ARG A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.598A pdb=" N GLU A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.818A pdb=" N ALA A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 892 removed outlier: 4.037A pdb=" N ALA A 890 " --> pdb=" O GLY A 886 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 919 through 927 removed outlier: 3.577A pdb=" N LEU A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 947 removed outlier: 4.010A pdb=" N THR A 946 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 947 " --> pdb=" O ILE A 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 943 through 947' Processing helix chain 'A' and resid 952 through 965 removed outlier: 3.519A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 1048 through 1053 removed outlier: 3.514A pdb=" N GLU A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1048 through 1053' Processing helix chain 'A' and resid 1089 through 1099 removed outlier: 3.969A pdb=" N LEU A1096 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A1097 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A1098 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 removed outlier: 3.875A pdb=" N LEU B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 599 removed outlier: 3.909A pdb=" N ASP B 596 " --> pdb=" O HIS B 592 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 597 " --> pdb=" O GLN B 593 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 640 removed outlier: 5.040A pdb=" N VAL B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 673 removed outlier: 3.639A pdb=" N GLN B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 682 Processing helix chain 'B' and resid 682 through 687 removed outlier: 3.523A pdb=" N ASN B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 709 removed outlier: 3.790A pdb=" N VAL B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 removed outlier: 4.136A pdb=" N GLN B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 807 removed outlier: 3.954A pdb=" N THR B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 794 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 795 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 796 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 801 " --> pdb=" O GLN B 797 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 824 removed outlier: 4.541A pdb=" N GLN B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 842 removed outlier: 3.791A pdb=" N ASP B 835 " --> pdb=" O THR B 831 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 836 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLY B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 841 " --> pdb=" O GLY B 837 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 857 through 883 removed outlier: 3.533A pdb=" N GLU B 861 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 863 " --> pdb=" O PRO B 859 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Proline residue: B 870 - end of helix removed outlier: 4.240A pdb=" N ALA B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 892 removed outlier: 4.009A pdb=" N ALA B 890 " --> pdb=" O GLY B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 919 through 928 removed outlier: 3.598A pdb=" N LEU B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 927 " --> pdb=" O PHE B 923 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 947 removed outlier: 4.028A pdb=" N THR B 946 " --> pdb=" O THR B 943 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 947 " --> pdb=" O ILE B 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 943 through 947' Processing helix chain 'B' and resid 952 through 966 removed outlier: 3.596A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1097 removed outlier: 3.916A pdb=" N LEU B1096 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B1097 " --> pdb=" O LEU B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 589 removed outlier: 3.893A pdb=" N LEU C 587 " --> pdb=" O TYR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 599 removed outlier: 3.865A pdb=" N ASP C 596 " --> pdb=" O HIS C 592 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 597 " --> pdb=" O GLN C 593 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.506A pdb=" N ILE C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 673 removed outlier: 3.583A pdb=" N GLN C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 682 Processing helix chain 'C' and resid 682 through 688 removed outlier: 3.540A pdb=" N ASN C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 709 removed outlier: 3.833A pdb=" N THR C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 725 removed outlier: 4.048A pdb=" N GLN C 725 " --> pdb=" O THR C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 775 Processing helix chain 'C' and resid 787 through 806 removed outlier: 3.907A pdb=" N THR C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 794 " --> pdb=" O THR C 790 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 795 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 796 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 798 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 806 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 824 removed outlier: 4.554A pdb=" N GLN C 816 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR C 821 " --> pdb=" O MET C 817 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 842 removed outlier: 4.241A pdb=" N ARG C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP C 835 " --> pdb=" O THR C 831 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY C 837 " --> pdb=" O THR C 833 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 841 " --> pdb=" O GLY C 837 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 842 " --> pdb=" O SER C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 856 Processing helix chain 'C' and resid 857 through 882 removed outlier: 3.642A pdb=" N GLU C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 863 " --> pdb=" O PRO C 859 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 869 " --> pdb=" O GLN C 865 " (cutoff:3.500A) Proline residue: C 870 - end of helix removed outlier: 4.155A pdb=" N ALA C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 892 removed outlier: 4.077A pdb=" N ALA C 890 " --> pdb=" O GLY C 886 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 913 removed outlier: 4.074A pdb=" N ALA C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 removed outlier: 3.701A pdb=" N LEU C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 947 removed outlier: 3.987A pdb=" N THR C 946 " --> pdb=" O THR C 943 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 947 " --> pdb=" O ILE C 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 947' Processing helix chain 'C' and resid 952 through 965 removed outlier: 3.608A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1053 removed outlier: 3.952A pdb=" N ARG C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU C1050 " --> pdb=" O GLY C1046 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C1051 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C1052 " --> pdb=" O ILE C1048 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET C1053 " --> pdb=" O ARG C1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1045 through 1053' Processing helix chain 'C' and resid 1089 through 1097 removed outlier: 3.536A pdb=" N LEU C1093 " --> pdb=" O PRO C1090 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C1096 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C1097 " --> pdb=" O LEU C1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 599 removed outlier: 3.947A pdb=" N LEU D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL D 590 " --> pdb=" O MET D 586 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP D 596 " --> pdb=" O HIS D 592 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET D 597 " --> pdb=" O GLN D 593 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 629 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.505A pdb=" N SER D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 673 removed outlier: 3.548A pdb=" N GLN D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 682 Processing helix chain 'D' and resid 682 through 688 Processing helix chain 'D' and resid 696 through 709 removed outlier: 3.667A pdb=" N THR D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET D 707 " --> pdb=" O GLN D 703 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 725 removed outlier: 4.052A pdb=" N GLN D 725 " --> pdb=" O THR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 807 removed outlier: 3.761A pdb=" N THR D 793 " --> pdb=" O GLN D 789 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 795 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 798 " --> pdb=" O ARG D 794 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 806 " --> pdb=" O LEU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 824 removed outlier: 4.725A pdb=" N GLN D 816 " --> pdb=" O GLN D 812 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR D 821 " --> pdb=" O MET D 817 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 822 " --> pdb=" O LEU D 818 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 830 No H-bonds generated for 'chain 'D' and resid 828 through 830' Processing helix chain 'D' and resid 831 through 842 removed outlier: 3.830A pdb=" N ASP D 835 " --> pdb=" O THR D 831 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 836 " --> pdb=" O ASP D 832 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLY D 837 " --> pdb=" O THR D 833 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER D 838 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 841 " --> pdb=" O GLY D 837 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 Processing helix chain 'D' and resid 857 through 882 removed outlier: 3.600A pdb=" N ALA D 863 " --> pdb=" O PRO D 859 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 869 " --> pdb=" O GLN D 865 " (cutoff:3.500A) Proline residue: D 870 - end of helix removed outlier: 3.592A pdb=" N GLU D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA D 877 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 892 removed outlier: 4.196A pdb=" N ALA D 890 " --> pdb=" O GLY D 886 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 892 " --> pdb=" O ASN D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 913 Processing helix chain 'D' and resid 919 through 924 removed outlier: 3.698A pdb=" N LEU D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 966 removed outlier: 3.684A pdb=" N LEU D 956 " --> pdb=" O ASN D 952 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 964 " --> pdb=" O ASN D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1053 removed outlier: 3.681A pdb=" N MET D1053 " --> pdb=" O ARG D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1097 removed outlier: 3.964A pdb=" N LEU D1096 " --> pdb=" O LEU D1093 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D1097 " --> pdb=" O LEU D1094 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 589 removed outlier: 3.927A pdb=" N LEU E 587 " --> pdb=" O TYR E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 599 removed outlier: 3.932A pdb=" N ASP E 596 " --> pdb=" O HIS E 592 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET E 597 " --> pdb=" O GLN E 593 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 599 " --> pdb=" O ALA E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 630 Processing helix chain 'E' and resid 631 through 637 removed outlier: 3.617A pdb=" N ILE E 635 " --> pdb=" O VAL E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 673 removed outlier: 3.530A pdb=" N GLN E 668 " --> pdb=" O GLU E 664 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 670 " --> pdb=" O LEU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 682 through 688 Processing helix chain 'E' and resid 696 through 709 removed outlier: 3.664A pdb=" N VAL E 700 " --> pdb=" O MET E 696 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 705 " --> pdb=" O THR E 701 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 706 " --> pdb=" O GLU E 702 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET E 707 " --> pdb=" O GLN E 703 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 708 " --> pdb=" O LEU E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 725 removed outlier: 4.064A pdb=" N GLN E 725 " --> pdb=" O THR E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 775 Processing helix chain 'E' and resid 787 through 807 removed outlier: 3.796A pdb=" N THR E 793 " --> pdb=" O GLN E 789 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 794 " --> pdb=" O THR E 790 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 795 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 796 " --> pdb=" O LEU E 792 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 798 " --> pdb=" O ARG E 794 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA E 806 " --> pdb=" O LEU E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 810 through 824 removed outlier: 4.692A pdb=" N GLN E 816 " --> pdb=" O GLN E 812 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR E 821 " --> pdb=" O MET E 817 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 822 " --> pdb=" O LEU E 818 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 823 " --> pdb=" O ALA E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 842 removed outlier: 4.124A pdb=" N ARG E 834 " --> pdb=" O LEU E 830 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP E 835 " --> pdb=" O THR E 831 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR E 836 " --> pdb=" O ASP E 832 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY E 837 " --> pdb=" O THR E 833 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER E 838 " --> pdb=" O ARG E 834 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 842 " --> pdb=" O SER E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 856 Processing helix chain 'E' and resid 857 through 883 removed outlier: 3.570A pdb=" N GLU E 861 " --> pdb=" O VAL E 857 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 863 " --> pdb=" O PRO E 859 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 869 " --> pdb=" O GLN E 865 " (cutoff:3.500A) Proline residue: E 870 - end of helix removed outlier: 4.170A pdb=" N ALA E 877 " --> pdb=" O GLU E 873 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 883 " --> pdb=" O TRP E 879 " (cutoff:3.500A) Processing helix chain 'E' and resid 883 through 892 removed outlier: 4.111A pdb=" N ALA E 890 " --> pdb=" O GLY E 886 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 892 " --> pdb=" O ASN E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 908 through 913 Processing helix chain 'E' and resid 919 through 927 removed outlier: 3.608A pdb=" N LEU E 924 " --> pdb=" O ILE E 920 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN E 925 " --> pdb=" O ALA E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 952 through 966 removed outlier: 3.594A pdb=" N LEU E 956 " --> pdb=" O ASN E 952 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN E 960 " --> pdb=" O LEU E 956 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 963 " --> pdb=" O ILE E 959 " (cutoff:3.500A) Processing helix chain 'E' and resid 1048 through 1053 removed outlier: 3.565A pdb=" N GLU E1052 " --> pdb=" O ILE E1048 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET E1053 " --> pdb=" O ARG E1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1048 through 1053' Processing helix chain 'E' and resid 1091 through 1097 removed outlier: 3.540A pdb=" N LEU E1094 " --> pdb=" O LEU E1091 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E1096 " --> pdb=" O LEU E1093 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG E1097 " --> pdb=" O LEU E1094 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 69 " --> pdb=" O TYR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'G' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 69 " --> pdb=" O TYR G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 79 Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE H 69 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE I 69 " --> pdb=" O TYR I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 79 Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU J 68 " --> pdb=" O ASP J 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE J 69 " --> pdb=" O TYR J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 79 Processing helix chain 'K' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU K 68 " --> pdb=" O ASP K 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 79 Processing helix chain 'L' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE L 69 " --> pdb=" O TYR L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 79 Processing helix chain 'M' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU M 68 " --> pdb=" O ASP M 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE M 69 " --> pdb=" O TYR M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 79 Processing helix chain 'N' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU N 68 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE N 69 " --> pdb=" O TYR N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'O' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE O 69 " --> pdb=" O TYR O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 79 Processing helix chain 'P' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU P 68 " --> pdb=" O ASP P 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 79 Processing helix chain 'Q' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU Q 68 " --> pdb=" O ASP Q 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE Q 69 " --> pdb=" O TYR Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 79 Processing helix chain 'R' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU R 68 " --> pdb=" O ASP R 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 79 Processing helix chain 'S' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU S 68 " --> pdb=" O ASP S 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 79 Processing helix chain 'T' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE T 69 " --> pdb=" O TYR T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 79 Processing helix chain 'a' and resid 570 through 577 Processing helix chain 'a' and resid 577 through 594 removed outlier: 5.794A pdb=" N TYR a 583 " --> pdb=" O ASP a 579 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN a 584 " --> pdb=" O ALA a 580 " (cutoff:3.500A) Processing helix chain 'a' and resid 598 through 603 removed outlier: 3.698A pdb=" N MET a 602 " --> pdb=" O ARG a 598 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR a 603 " --> pdb=" O LEU a 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 598 through 603' Processing helix chain 'a' and resid 625 through 630 removed outlier: 3.862A pdb=" N GLU a 629 " --> pdb=" O ALA a 626 " (cutoff:3.500A) Processing helix chain 'a' and resid 634 through 643 removed outlier: 3.599A pdb=" N ILE a 639 " --> pdb=" O ILE a 635 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN a 640 " --> pdb=" O ASP a 636 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU a 641 " --> pdb=" O THR a 637 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG a 642 " --> pdb=" O VAL a 638 " (cutoff:3.500A) Processing helix chain 'a' and resid 666 through 687 removed outlier: 3.860A pdb=" N ARG a 673 " --> pdb=" O ARG a 669 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY a 679 " --> pdb=" O PHE a 675 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN a 680 " --> pdb=" O ALA a 676 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN a 684 " --> pdb=" O ASN a 680 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE a 685 " --> pdb=" O ALA a 681 " (cutoff:3.500A) Processing helix chain 'a' and resid 699 through 704 removed outlier: 4.266A pdb=" N GLN a 703 " --> pdb=" O ASP a 699 " (cutoff:3.500A) Processing helix chain 'a' and resid 715 through 728 removed outlier: 3.603A pdb=" N ARG a 727 " --> pdb=" O ALA a 723 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR a 728 " --> pdb=" O VAL a 724 " (cutoff:3.500A) Processing helix chain 'a' and resid 765 through 770 removed outlier: 4.079A pdb=" N PHE a 769 " --> pdb=" O LEU a 765 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY a 770 " --> pdb=" O ALA a 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 765 through 770' Processing helix chain 'a' and resid 784 through 804 removed outlier: 4.636A pdb=" N LEU a 788 " --> pdb=" O ASP a 784 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR a 793 " --> pdb=" O GLN a 789 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG a 801 " --> pdb=" O GLN a 797 " (cutoff:3.500A) Processing helix chain 'a' and resid 810 through 824 removed outlier: 3.881A pdb=" N MET a 814 " --> pdb=" O ASP a 810 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET a 817 " --> pdb=" O ALA a 813 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU a 823 " --> pdb=" O ALA a 819 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN a 824 " --> pdb=" O GLN a 820 " (cutoff:3.500A) Processing helix chain 'a' and resid 828 through 843 removed outlier: 3.756A pdb=" N ASP a 832 " --> pdb=" O VAL a 828 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR a 833 " --> pdb=" O ASP a 829 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG a 834 " --> pdb=" O LEU a 830 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU a 839 " --> pdb=" O ASP a 835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR a 840 " --> pdb=" O TYR a 836 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA a 841 " --> pdb=" O GLY a 837 " (cutoff:3.500A) Processing helix chain 'a' and resid 848 through 853 Processing helix chain 'a' and resid 857 through 865 removed outlier: 3.623A pdb=" N GLU a 861 " --> pdb=" O VAL a 857 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN a 862 " --> pdb=" O ARG a 858 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA a 863 " --> pdb=" O PRO a 859 " (cutoff:3.500A) Processing helix chain 'a' and resid 867 through 883 removed outlier: 3.538A pdb=" N ALA a 871 " --> pdb=" O VAL a 867 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU a 875 " --> pdb=" O ALA a 871 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN a 876 " --> pdb=" O ALA a 872 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA a 877 " --> pdb=" O GLU a 873 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR a 881 " --> pdb=" O ALA a 877 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL a 883 " --> pdb=" O TRP a 879 " (cutoff:3.500A) Processing helix chain 'a' and resid 883 through 890 removed outlier: 3.741A pdb=" N ALA a 890 " --> pdb=" O GLY a 886 " (cutoff:3.500A) Processing helix chain 'a' and resid 894 through 898 removed outlier: 4.055A pdb=" N PHE a 897 " --> pdb=" O ARG a 894 " (cutoff:3.500A) Processing helix chain 'a' and resid 905 through 910 removed outlier: 3.861A pdb=" N LEU a 909 " --> pdb=" O SER a 905 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA a 910 " --> pdb=" O LEU a 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 905 through 910' Processing helix chain 'a' and resid 952 through 967 removed outlier: 3.744A pdb=" N LEU a 956 " --> pdb=" O ASN a 952 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN a 960 " --> pdb=" O LEU a 956 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU a 962 " --> pdb=" O ALA a 958 " (cutoff:3.500A) Processing helix chain 'a' and resid 1046 through 1051 removed outlier: 3.690A pdb=" N LEU a1050 " --> pdb=" O GLY a1046 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU a1051 " --> pdb=" O LEU a1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1046 through 1051' Processing helix chain 'a' and resid 1052 through 1055 removed outlier: 4.057A pdb=" N ARG a1055 " --> pdb=" O GLU a1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1052 through 1055' Processing helix chain 'a' and resid 1072 through 1076 removed outlier: 4.145A pdb=" N GLY a1075 " --> pdb=" O ALA a1072 " (cutoff:3.500A) Processing helix chain 'a' and resid 1088 through 1097 removed outlier: 3.695A pdb=" N LEU a1091 " --> pdb=" O GLU a1088 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL a1092 " --> pdb=" O GLY a1089 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU a1093 " --> pdb=" O PRO a1090 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU a1096 " --> pdb=" O LEU a1093 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG a1097 " --> pdb=" O LEU a1094 " (cutoff:3.500A) Processing helix chain 'a' and resid 1117 through 1129 removed outlier: 4.598A pdb=" N ASP a1123 " --> pdb=" O GLU a1119 " (cutoff:3.500A) Processing helix chain 'b' and resid 570 through 577 Processing helix chain 'b' and resid 577 through 594 removed outlier: 5.800A pdb=" N TYR b 583 " --> pdb=" O ASP b 579 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN b 584 " --> pdb=" O ALA b 580 " (cutoff:3.500A) Processing helix chain 'b' and resid 598 through 603 removed outlier: 3.620A pdb=" N MET b 602 " --> pdb=" O ARG b 598 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR b 603 " --> pdb=" O LEU b 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 598 through 603' Processing helix chain 'b' and resid 634 through 643 removed outlier: 3.524A pdb=" N ILE b 639 " --> pdb=" O ILE b 635 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN b 640 " --> pdb=" O ASP b 636 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU b 641 " --> pdb=" O THR b 637 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG b 642 " --> pdb=" O VAL b 638 " (cutoff:3.500A) Processing helix chain 'b' and resid 664 through 687 removed outlier: 4.061A pdb=" N ARG b 669 " --> pdb=" O ALA b 665 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG b 673 " --> pdb=" O ARG b 669 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY b 679 " --> pdb=" O PHE b 675 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN b 680 " --> pdb=" O ALA b 676 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP b 682 " --> pdb=" O PHE b 678 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN b 684 " --> pdb=" O ASN b 680 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE b 685 " --> pdb=" O ALA b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 699 through 706 removed outlier: 4.168A pdb=" N GLN b 703 " --> pdb=" O ASP b 699 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR b 705 " --> pdb=" O THR b 701 " (cutoff:3.500A) Processing helix chain 'b' and resid 715 through 728 removed outlier: 3.637A pdb=" N THR b 728 " --> pdb=" O VAL b 724 " (cutoff:3.500A) Processing helix chain 'b' and resid 784 through 804 removed outlier: 4.576A pdb=" N LEU b 788 " --> pdb=" O ASP b 784 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR b 796 " --> pdb=" O LEU b 792 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG b 801 " --> pdb=" O GLN b 797 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN b 804 " --> pdb=" O LEU b 800 " (cutoff:3.500A) Processing helix chain 'b' and resid 810 through 824 removed outlier: 4.039A pdb=" N MET b 814 " --> pdb=" O ASP b 810 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR b 821 " --> pdb=" O MET b 817 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL b 822 " --> pdb=" O LEU b 818 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU b 823 " --> pdb=" O ALA b 819 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN b 824 " --> pdb=" O GLN b 820 " (cutoff:3.500A) Processing helix chain 'b' and resid 828 through 840 removed outlier: 3.662A pdb=" N ASP b 832 " --> pdb=" O VAL b 828 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR b 833 " --> pdb=" O ASP b 829 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG b 834 " --> pdb=" O LEU b 830 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP b 835 " --> pdb=" O THR b 831 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER b 838 " --> pdb=" O ARG b 834 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU b 839 " --> pdb=" O ASP b 835 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR b 840 " --> pdb=" O TYR b 836 " (cutoff:3.500A) Processing helix chain 'b' and resid 848 through 853 Processing helix chain 'b' and resid 857 through 865 removed outlier: 3.613A pdb=" N GLU b 861 " --> pdb=" O VAL b 857 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN b 862 " --> pdb=" O ARG b 858 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA b 863 " --> pdb=" O PRO b 859 " (cutoff:3.500A) Processing helix chain 'b' and resid 867 through 883 removed outlier: 4.066A pdb=" N ASN b 876 " --> pdb=" O ALA b 872 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA b 877 " --> pdb=" O GLU b 873 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR b 881 " --> pdb=" O ALA b 877 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL b 883 " --> pdb=" O TRP b 879 " (cutoff:3.500A) Processing helix chain 'b' and resid 883 through 891 removed outlier: 4.491A pdb=" N ASN b 889 " --> pdb=" O ASP b 885 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE b 891 " --> pdb=" O TRP b 887 " (cutoff:3.500A) Processing helix chain 'b' and resid 894 through 898 removed outlier: 4.119A pdb=" N PHE b 897 " --> pdb=" O ARG b 894 " (cutoff:3.500A) Processing helix chain 'b' and resid 905 through 910 removed outlier: 3.733A pdb=" N LEU b 909 " --> pdb=" O SER b 905 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA b 910 " --> pdb=" O LEU b 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 905 through 910' Processing helix chain 'b' and resid 952 through 967 removed outlier: 3.759A pdb=" N LEU b 956 " --> pdb=" O ASN b 952 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU b 962 " --> pdb=" O ALA b 958 " (cutoff:3.500A) Processing helix chain 'b' and resid 1046 through 1051 removed outlier: 3.772A pdb=" N LEU b1050 " --> pdb=" O GLY b1046 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU b1051 " --> pdb=" O LEU b1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1046 through 1051' Processing helix chain 'b' and resid 1052 through 1055 removed outlier: 4.264A pdb=" N ARG b1055 " --> pdb=" O GLU b1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1052 through 1055' Processing helix chain 'b' and resid 1072 through 1076 removed outlier: 4.313A pdb=" N GLY b1075 " --> pdb=" O ALA b1072 " (cutoff:3.500A) Processing helix chain 'b' and resid 1088 through 1097 removed outlier: 3.511A pdb=" N LEU b1091 " --> pdb=" O GLU b1088 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL b1092 " --> pdb=" O GLY b1089 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU b1093 " --> pdb=" O PRO b1090 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU b1096 " --> pdb=" O LEU b1093 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG b1097 " --> pdb=" O LEU b1094 " (cutoff:3.500A) Processing helix chain 'b' and resid 1117 through 1129 removed outlier: 4.659A pdb=" N ASP b1123 " --> pdb=" O GLU b1119 " (cutoff:3.500A) Processing helix chain 'c' and resid 570 through 577 Processing helix chain 'c' and resid 577 through 594 removed outlier: 5.890A pdb=" N TYR c 583 " --> pdb=" O ASP c 579 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN c 584 " --> pdb=" O ALA c 580 " (cutoff:3.500A) Processing helix chain 'c' and resid 598 through 603 removed outlier: 3.611A pdb=" N MET c 602 " --> pdb=" O ARG c 598 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR c 603 " --> pdb=" O LEU c 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 598 through 603' Processing helix chain 'c' and resid 634 through 643 removed outlier: 3.887A pdb=" N ASN c 640 " --> pdb=" O ASP c 636 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU c 641 " --> pdb=" O THR c 637 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG c 642 " --> pdb=" O VAL c 638 " (cutoff:3.500A) Processing helix chain 'c' and resid 664 through 687 removed outlier: 3.853A pdb=" N ARG c 669 " --> pdb=" O ALA c 665 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG c 673 " --> pdb=" O ARG c 669 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY c 679 " --> pdb=" O PHE c 675 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN c 680 " --> pdb=" O ALA c 676 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN c 684 " --> pdb=" O ASN c 680 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE c 685 " --> pdb=" O ALA c 681 " (cutoff:3.500A) Processing helix chain 'c' and resid 699 through 706 removed outlier: 4.206A pdb=" N GLN c 703 " --> pdb=" O ASP c 699 " (cutoff:3.500A) Processing helix chain 'c' and resid 715 through 728 removed outlier: 3.619A pdb=" N THR c 728 " --> pdb=" O VAL c 724 " (cutoff:3.500A) Processing helix chain 'c' and resid 765 through 770 removed outlier: 3.818A pdb=" N PHE c 769 " --> pdb=" O LEU c 765 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY c 770 " --> pdb=" O ALA c 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 765 through 770' Processing helix chain 'c' and resid 784 through 804 removed outlier: 4.587A pdb=" N LEU c 788 " --> pdb=" O ASP c 784 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR c 793 " --> pdb=" O GLN c 789 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG c 801 " --> pdb=" O GLN c 797 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN c 804 " --> pdb=" O LEU c 800 " (cutoff:3.500A) Processing helix chain 'c' and resid 810 through 824 removed outlier: 3.862A pdb=" N MET c 814 " --> pdb=" O ASP c 810 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN c 816 " --> pdb=" O GLN c 812 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET c 817 " --> pdb=" O ALA c 813 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU c 823 " --> pdb=" O ALA c 819 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN c 824 " --> pdb=" O GLN c 820 " (cutoff:3.500A) Processing helix chain 'c' and resid 828 through 843 removed outlier: 3.589A pdb=" N THR c 833 " --> pdb=" O ASP c 829 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG c 834 " --> pdb=" O LEU c 830 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP c 835 " --> pdb=" O THR c 831 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU c 839 " --> pdb=" O ASP c 835 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR c 840 " --> pdb=" O TYR c 836 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA c 841 " --> pdb=" O GLY c 837 " (cutoff:3.500A) Processing helix chain 'c' and resid 848 through 853 Processing helix chain 'c' and resid 857 through 865 removed outlier: 3.573A pdb=" N GLU c 861 " --> pdb=" O VAL c 857 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN c 862 " --> pdb=" O ARG c 858 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA c 863 " --> pdb=" O PRO c 859 " (cutoff:3.500A) Processing helix chain 'c' and resid 867 through 883 removed outlier: 3.543A pdb=" N ALA c 871 " --> pdb=" O VAL c 867 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU c 873 " --> pdb=" O THR c 869 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN c 876 " --> pdb=" O ALA c 872 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA c 877 " --> pdb=" O GLU c 873 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR c 881 " --> pdb=" O ALA c 877 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL c 883 " --> pdb=" O TRP c 879 " (cutoff:3.500A) Processing helix chain 'c' and resid 883 through 891 removed outlier: 4.437A pdb=" N ASN c 889 " --> pdb=" O ASP c 885 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE c 891 " --> pdb=" O TRP c 887 " (cutoff:3.500A) Processing helix chain 'c' and resid 894 through 898 removed outlier: 4.060A pdb=" N PHE c 897 " --> pdb=" O ARG c 894 " (cutoff:3.500A) Processing helix chain 'c' and resid 905 through 910 removed outlier: 3.825A pdb=" N LEU c 909 " --> pdb=" O SER c 905 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA c 910 " --> pdb=" O LEU c 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 905 through 910' Processing helix chain 'c' and resid 952 through 967 removed outlier: 3.790A pdb=" N LEU c 956 " --> pdb=" O ASN c 952 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU c 962 " --> pdb=" O ALA c 958 " (cutoff:3.500A) Processing helix chain 'c' and resid 1051 through 1055 removed outlier: 4.008A pdb=" N ALA c1054 " --> pdb=" O LEU c1051 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG c1055 " --> pdb=" O GLU c1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 1051 through 1055' Processing helix chain 'c' and resid 1072 through 1076 removed outlier: 4.209A pdb=" N GLY c1075 " --> pdb=" O ALA c1072 " (cutoff:3.500A) Processing helix chain 'c' and resid 1088 through 1096 removed outlier: 3.630A pdb=" N LEU c1091 " --> pdb=" O GLU c1088 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU c1093 " --> pdb=" O PRO c1090 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU c1094 " --> pdb=" O LEU c1091 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU c1096 " --> pdb=" O LEU c1093 " (cutoff:3.500A) Processing helix chain 'c' and resid 1117 through 1129 removed outlier: 4.622A pdb=" N ASP c1123 " --> pdb=" O GLU c1119 " (cutoff:3.500A) Processing helix chain 'd' and resid 572 through 577 Processing helix chain 'd' and resid 577 through 594 removed outlier: 5.951A pdb=" N TYR d 583 " --> pdb=" O ASP d 579 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN d 584 " --> pdb=" O ALA d 580 " (cutoff:3.500A) Processing helix chain 'd' and resid 598 through 603 removed outlier: 3.589A pdb=" N MET d 602 " --> pdb=" O ARG d 598 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR d 603 " --> pdb=" O LEU d 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 598 through 603' Processing helix chain 'd' and resid 634 through 643 removed outlier: 3.530A pdb=" N ILE d 639 " --> pdb=" O ILE d 635 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN d 640 " --> pdb=" O ASP d 636 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU d 641 " --> pdb=" O THR d 637 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG d 642 " --> pdb=" O VAL d 638 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG d 643 " --> pdb=" O ILE d 639 " (cutoff:3.500A) Processing helix chain 'd' and resid 666 through 687 removed outlier: 3.804A pdb=" N ARG d 673 " --> pdb=" O ARG d 669 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY d 679 " --> pdb=" O PHE d 675 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN d 680 " --> pdb=" O ALA d 676 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN d 684 " --> pdb=" O ASN d 680 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE d 685 " --> pdb=" O ALA d 681 " (cutoff:3.500A) Processing helix chain 'd' and resid 699 through 704 removed outlier: 4.122A pdb=" N GLN d 703 " --> pdb=" O ASP d 699 " (cutoff:3.500A) Processing helix chain 'd' and resid 715 through 728 removed outlier: 3.623A pdb=" N THR d 728 " --> pdb=" O VAL d 724 " (cutoff:3.500A) Processing helix chain 'd' and resid 765 through 770 removed outlier: 4.079A pdb=" N PHE d 769 " --> pdb=" O LEU d 765 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY d 770 " --> pdb=" O ALA d 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 765 through 770' Processing helix chain 'd' and resid 784 through 804 removed outlier: 4.624A pdb=" N LEU d 788 " --> pdb=" O ASP d 784 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR d 793 " --> pdb=" O GLN d 789 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN d 804 " --> pdb=" O LEU d 800 " (cutoff:3.500A) Processing helix chain 'd' and resid 810 through 824 removed outlier: 4.058A pdb=" N MET d 814 " --> pdb=" O ASP d 810 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU d 823 " --> pdb=" O ALA d 819 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN d 824 " --> pdb=" O GLN d 820 " (cutoff:3.500A) Processing helix chain 'd' and resid 828 through 843 removed outlier: 3.619A pdb=" N ASP d 832 " --> pdb=" O VAL d 828 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR d 833 " --> pdb=" O ASP d 829 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG d 834 " --> pdb=" O LEU d 830 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU d 839 " --> pdb=" O ASP d 835 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR d 840 " --> pdb=" O TYR d 836 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA d 841 " --> pdb=" O GLY d 837 " (cutoff:3.500A) Processing helix chain 'd' and resid 848 through 853 Processing helix chain 'd' and resid 857 through 865 removed outlier: 3.533A pdb=" N GLU d 861 " --> pdb=" O VAL d 857 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN d 862 " --> pdb=" O ARG d 858 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA d 863 " --> pdb=" O PRO d 859 " (cutoff:3.500A) Processing helix chain 'd' and resid 867 through 883 removed outlier: 4.074A pdb=" N ASN d 876 " --> pdb=" O ALA d 872 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA d 877 " --> pdb=" O GLU d 873 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR d 881 " --> pdb=" O ALA d 877 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL d 883 " --> pdb=" O TRP d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 883 through 891 removed outlier: 3.781A pdb=" N PHE d 891 " --> pdb=" O TRP d 887 " (cutoff:3.500A) Processing helix chain 'd' and resid 905 through 910 removed outlier: 3.832A pdb=" N LEU d 909 " --> pdb=" O SER d 905 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA d 910 " --> pdb=" O LEU d 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 905 through 910' Processing helix chain 'd' and resid 952 through 967 removed outlier: 3.857A pdb=" N LEU d 956 " --> pdb=" O ASN d 952 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA d 958 " --> pdb=" O ALA d 954 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU d 962 " --> pdb=" O ALA d 958 " (cutoff:3.500A) Processing helix chain 'd' and resid 1046 through 1051 removed outlier: 3.649A pdb=" N LEU d1050 " --> pdb=" O GLY d1046 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU d1051 " --> pdb=" O LEU d1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1046 through 1051' Processing helix chain 'd' and resid 1052 through 1055 removed outlier: 4.085A pdb=" N ARG d1055 " --> pdb=" O GLU d1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1052 through 1055' Processing helix chain 'd' and resid 1072 through 1076 removed outlier: 4.314A pdb=" N GLY d1075 " --> pdb=" O ALA d1072 " (cutoff:3.500A) Processing helix chain 'd' and resid 1088 through 1097 removed outlier: 3.576A pdb=" N LEU d1091 " --> pdb=" O GLU d1088 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL d1092 " --> pdb=" O GLY d1089 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU d1093 " --> pdb=" O PRO d1090 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU d1096 " --> pdb=" O LEU d1093 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG d1097 " --> pdb=" O LEU d1094 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1127 removed outlier: 4.688A pdb=" N ASP d1123 " --> pdb=" O GLU d1119 " (cutoff:3.500A) Processing helix chain 'e' and resid 570 through 577 Processing helix chain 'e' and resid 577 through 594 removed outlier: 5.964A pdb=" N TYR e 583 " --> pdb=" O ASP e 579 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN e 584 " --> pdb=" O ALA e 580 " (cutoff:3.500A) Processing helix chain 'e' and resid 598 through 603 removed outlier: 3.756A pdb=" N THR e 603 " --> pdb=" O LEU e 599 " (cutoff:3.500A) Processing helix chain 'e' and resid 625 through 630 removed outlier: 3.809A pdb=" N GLU e 629 " --> pdb=" O ALA e 626 " (cutoff:3.500A) Processing helix chain 'e' and resid 634 through 643 removed outlier: 3.670A pdb=" N ILE e 639 " --> pdb=" O ILE e 635 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN e 640 " --> pdb=" O ASP e 636 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU e 641 " --> pdb=" O THR e 637 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG e 642 " --> pdb=" O VAL e 638 " (cutoff:3.500A) Processing helix chain 'e' and resid 664 through 687 removed outlier: 3.997A pdb=" N ARG e 669 " --> pdb=" O ALA e 665 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG e 673 " --> pdb=" O ARG e 669 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY e 679 " --> pdb=" O PHE e 675 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN e 680 " --> pdb=" O ALA e 676 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN e 684 " --> pdb=" O ASN e 680 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE e 685 " --> pdb=" O ALA e 681 " (cutoff:3.500A) Processing helix chain 'e' and resid 699 through 704 removed outlier: 4.256A pdb=" N GLN e 703 " --> pdb=" O ASP e 699 " (cutoff:3.500A) Processing helix chain 'e' and resid 715 through 728 removed outlier: 3.610A pdb=" N THR e 728 " --> pdb=" O VAL e 724 " (cutoff:3.500A) Processing helix chain 'e' and resid 765 through 770 removed outlier: 3.644A pdb=" N PHE e 769 " --> pdb=" O LEU e 765 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY e 770 " --> pdb=" O ALA e 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 765 through 770' Processing helix chain 'e' and resid 784 through 804 removed outlier: 4.413A pdb=" N LEU e 788 " --> pdb=" O ASP e 784 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR e 793 " --> pdb=" O GLN e 789 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN e 804 " --> pdb=" O LEU e 800 " (cutoff:3.500A) Processing helix chain 'e' and resid 811 through 824 removed outlier: 3.892A pdb=" N MET e 817 " --> pdb=" O ALA e 813 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU e 823 " --> pdb=" O ALA e 819 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN e 824 " --> pdb=" O GLN e 820 " (cutoff:3.500A) Processing helix chain 'e' and resid 828 through 840 removed outlier: 3.660A pdb=" N ASP e 832 " --> pdb=" O VAL e 828 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR e 833 " --> pdb=" O ASP e 829 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG e 834 " --> pdb=" O LEU e 830 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP e 835 " --> pdb=" O THR e 831 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER e 838 " --> pdb=" O ARG e 834 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU e 839 " --> pdb=" O ASP e 835 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR e 840 " --> pdb=" O TYR e 836 " (cutoff:3.500A) Processing helix chain 'e' and resid 848 through 853 Processing helix chain 'e' and resid 857 through 865 removed outlier: 3.704A pdb=" N GLU e 861 " --> pdb=" O VAL e 857 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN e 862 " --> pdb=" O ARG e 858 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA e 863 " --> pdb=" O PRO e 859 " (cutoff:3.500A) Processing helix chain 'e' and resid 867 through 883 removed outlier: 3.935A pdb=" N ALA e 871 " --> pdb=" O VAL e 867 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN e 876 " --> pdb=" O ALA e 872 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA e 877 " --> pdb=" O GLU e 873 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR e 881 " --> pdb=" O ALA e 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL e 883 " --> pdb=" O TRP e 879 " (cutoff:3.500A) Processing helix chain 'e' and resid 883 through 891 removed outlier: 3.994A pdb=" N ALA e 890 " --> pdb=" O GLY e 886 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE e 891 " --> pdb=" O TRP e 887 " (cutoff:3.500A) Processing helix chain 'e' and resid 894 through 898 removed outlier: 4.009A pdb=" N PHE e 897 " --> pdb=" O ARG e 894 " (cutoff:3.500A) Processing helix chain 'e' and resid 905 through 910 removed outlier: 3.716A pdb=" N LEU e 909 " --> pdb=" O SER e 905 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA e 910 " --> pdb=" O LEU e 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 905 through 910' Processing helix chain 'e' and resid 952 through 967 removed outlier: 3.826A pdb=" N LEU e 956 " --> pdb=" O ASN e 952 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA e 958 " --> pdb=" O ALA e 954 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU e 962 " --> pdb=" O ALA e 958 " (cutoff:3.500A) Processing helix chain 'e' and resid 1046 through 1051 removed outlier: 3.521A pdb=" N LEU e1051 " --> pdb=" O LEU e1047 " (cutoff:3.500A) Processing helix chain 'e' and resid 1072 through 1076 removed outlier: 4.262A pdb=" N GLY e1075 " --> pdb=" O ALA e1072 " (cutoff:3.500A) Processing helix chain 'e' and resid 1088 through 1097 removed outlier: 3.574A pdb=" N LEU e1091 " --> pdb=" O GLU e1088 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL e1092 " --> pdb=" O GLY e1089 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU e1093 " --> pdb=" O PRO e1090 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU e1096 " --> pdb=" O LEU e1093 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG e1097 " --> pdb=" O LEU e1094 " (cutoff:3.500A) Processing helix chain 'e' and resid 1117 through 1127 removed outlier: 4.621A pdb=" N ASP e1123 " --> pdb=" O GLU e1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1011 through 1012 removed outlier: 3.830A pdb=" N TYR A1080 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A1065 " --> pdb=" O ALA A1059 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1024 through 1029 removed outlier: 7.344A pdb=" N ALA A1024 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP A1040 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A1026 " --> pdb=" O TYR A1038 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A1038 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 6.093A pdb=" N ARG B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA B1072 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP B1070 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B1080 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B1065 " --> pdb=" O ALA B1059 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B1067 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1024 through 1025 removed outlier: 4.036A pdb=" N ALA B1024 " --> pdb=" O LEU B1041 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B1041 " --> pdb=" O ALA B1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 1028 through 1029 Processing sheet with id=AA6, first strand: chain 'C' and resid 1011 through 1012 removed outlier: 3.700A pdb=" N TYR C1080 " --> pdb=" O LEU C1068 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C1065 " --> pdb=" O ALA C1059 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 1024 through 1029 removed outlier: 7.397A pdb=" N ALA C1024 " --> pdb=" O ASP C1040 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP C1040 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C1026 " --> pdb=" O TYR C1038 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C1038 " --> pdb=" O LEU C1026 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1011 through 1012 removed outlier: 3.849A pdb=" N TYR D1080 " --> pdb=" O LEU D1068 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D1065 " --> pdb=" O ALA D1059 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1024 through 1029 removed outlier: 7.291A pdb=" N ALA D1024 " --> pdb=" O ASP D1040 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP D1040 " --> pdb=" O ALA D1024 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU D1026 " --> pdb=" O TYR D1038 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR D1038 " --> pdb=" O LEU D1026 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1011 through 1012 removed outlier: 3.508A pdb=" N LYS E1011 " --> pdb=" O LEU E 981 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 981 " --> pdb=" O LYS E1011 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E1080 " --> pdb=" O LEU E1068 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY E1065 " --> pdb=" O ALA E1059 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E1059 " --> pdb=" O GLY E1065 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1024 through 1029 removed outlier: 7.384A pdb=" N ALA E1024 " --> pdb=" O ASP E1040 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP E1040 " --> pdb=" O ALA E1024 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E1026 " --> pdb=" O TYR E1038 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR E1038 " --> pdb=" O LEU E1026 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL F 94 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 30 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY F 144 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA F 35 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU F 139 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN F 53 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN F 83 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE F 51 " --> pdb=" O GLN F 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP F 85 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL F 49 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP F 87 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL F 47 " --> pdb=" O TRP F 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL G 94 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 30 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY G 144 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA G 35 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU G 139 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN G 53 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN G 83 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE G 51 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP G 85 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 49 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP G 87 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL G 47 " --> pdb=" O TRP G 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL H 94 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE H 30 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY H 144 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA H 35 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU H 139 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN H 53 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN H 83 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE H 51 " --> pdb=" O GLN H 83 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP H 85 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL H 49 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP H 87 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL H 47 " --> pdb=" O TRP H 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL I 94 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE I 30 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY I 144 " --> pdb=" O ARG I 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA I 35 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU I 139 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN I 53 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN I 83 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE I 51 " --> pdb=" O GLN I 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP I 85 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL I 49 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP I 87 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL I 47 " --> pdb=" O TRP I 87 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 94 through 99 removed outlier: 3.665A pdb=" N VAL J 94 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE J 30 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY J 144 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA J 35 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU J 139 " --> pdb=" O LEU J 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN J 53 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN J 83 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE J 51 " --> pdb=" O GLN J 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP J 85 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL J 49 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP J 87 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL J 47 " --> pdb=" O TRP J 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL K 94 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE K 30 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY K 144 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA K 35 " --> pdb=" O GLY K 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU K 139 " --> pdb=" O LEU K 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN K 53 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN K 83 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE K 51 " --> pdb=" O GLN K 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP K 85 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL K 49 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP K 87 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL K 47 " --> pdb=" O TRP K 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL L 94 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE L 30 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY L 144 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA L 35 " --> pdb=" O GLY L 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU L 139 " --> pdb=" O LEU L 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN L 53 " --> pdb=" O ILE L 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN L 83 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE L 51 " --> pdb=" O GLN L 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP L 85 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL L 49 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP L 87 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL L 47 " --> pdb=" O TRP L 87 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL M 94 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE M 30 " --> pdb=" O VAL M 94 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY M 144 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA M 35 " --> pdb=" O GLY M 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU M 139 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN M 53 " --> pdb=" O ILE M 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN M 83 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE M 51 " --> pdb=" O GLN M 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP M 85 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL M 49 " --> pdb=" O ASP M 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP M 87 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL M 47 " --> pdb=" O TRP M 87 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL N 94 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE N 30 " --> pdb=" O VAL N 94 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY N 144 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA N 35 " --> pdb=" O GLY N 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU N 139 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN N 53 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN N 83 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE N 51 " --> pdb=" O GLN N 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP N 85 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL N 49 " --> pdb=" O ASP N 85 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP N 87 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL N 47 " --> pdb=" O TRP N 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL O 94 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE O 30 " --> pdb=" O VAL O 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY O 144 " --> pdb=" O ARG O 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA O 35 " --> pdb=" O GLY O 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU O 139 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN O 53 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN O 83 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE O 51 " --> pdb=" O GLN O 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP O 85 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL O 49 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP O 87 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL O 47 " --> pdb=" O TRP O 87 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL P 94 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE P 30 " --> pdb=" O VAL P 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY P 144 " --> pdb=" O ARG P 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA P 35 " --> pdb=" O GLY P 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU P 139 " --> pdb=" O LEU P 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN P 53 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN P 83 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE P 51 " --> pdb=" O GLN P 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP P 85 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL P 49 " --> pdb=" O ASP P 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP P 87 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL P 47 " --> pdb=" O TRP P 87 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL Q 94 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE Q 30 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY Q 144 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA Q 35 " --> pdb=" O GLY Q 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU Q 139 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN Q 53 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN Q 83 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE Q 51 " --> pdb=" O GLN Q 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP Q 85 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL Q 49 " --> pdb=" O ASP Q 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP Q 87 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL Q 47 " --> pdb=" O TRP Q 87 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL R 94 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 30 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY R 144 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA R 35 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU R 139 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN R 53 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN R 83 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE R 51 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP R 85 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL R 49 " --> pdb=" O ASP R 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP R 87 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL R 47 " --> pdb=" O TRP R 87 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL S 94 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE S 30 " --> pdb=" O VAL S 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY S 144 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA S 35 " --> pdb=" O GLY S 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU S 139 " --> pdb=" O LEU S 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 80 through 88 removed outlier: 6.795A pdb=" N GLN S 53 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN S 83 " --> pdb=" O ILE S 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE S 51 " --> pdb=" O GLN S 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP S 85 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL S 49 " --> pdb=" O ASP S 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP S 87 " --> pdb=" O VAL S 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL S 47 " --> pdb=" O TRP S 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL T 94 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE T 30 " --> pdb=" O VAL T 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY T 144 " --> pdb=" O ARG T 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA T 35 " --> pdb=" O GLY T 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU T 139 " --> pdb=" O LEU T 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN T 53 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN T 83 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE T 51 " --> pdb=" O GLN T 83 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP T 85 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL T 49 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP T 87 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL T 47 " --> pdb=" O TRP T 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 933 through 935 removed outlier: 3.921A pdb=" N HIS a 933 " --> pdb=" O VAL a 940 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL a 940 " --> pdb=" O HIS a 933 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU a 935 " --> pdb=" O ARG a 938 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'a' and resid 978 through 980 Processing sheet with id=AE8, first strand: chain 'a' and resid 999 through 1001 removed outlier: 3.793A pdb=" N THR a 996 " --> pdb=" O GLN a 999 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN a 991 " --> pdb=" O VAL a1029 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA a1024 " --> pdb=" O ASP a1040 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP a1040 " --> pdb=" O ALA a1024 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU a1026 " --> pdb=" O TYR a1038 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP a1028 " --> pdb=" O ARG a1036 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 1066 through 1068 Processing sheet with id=AF1, first strand: chain 'b' and resid 933 through 935 removed outlier: 3.970A pdb=" N HIS b 933 " --> pdb=" O VAL b 940 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL b 940 " --> pdb=" O HIS b 933 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU b 935 " --> pdb=" O ARG b 938 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 978 through 981 removed outlier: 3.634A pdb=" N LYS b1011 " --> pdb=" O LEU b 981 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 999 through 1001 removed outlier: 4.084A pdb=" N THR b 996 " --> pdb=" O GLN b 999 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN b 991 " --> pdb=" O VAL b1029 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA b1024 " --> pdb=" O ASP b1040 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP b1040 " --> pdb=" O ALA b1024 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU b1026 " --> pdb=" O TYR b1038 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP b1028 " --> pdb=" O ARG b1036 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 1066 through 1068 Processing sheet with id=AF5, first strand: chain 'c' and resid 933 through 935 removed outlier: 3.868A pdb=" N HIS c 933 " --> pdb=" O VAL c 940 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL c 940 " --> pdb=" O HIS c 933 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU c 935 " --> pdb=" O ARG c 938 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 978 through 980 Processing sheet with id=AF7, first strand: chain 'c' and resid 999 through 1003 removed outlier: 3.773A pdb=" N THR c 996 " --> pdb=" O GLN c 999 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN c 991 " --> pdb=" O VAL c1029 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP c1028 " --> pdb=" O ARG c1036 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG c1036 " --> pdb=" O TRP c1028 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 999 through 1003 removed outlier: 3.773A pdb=" N THR c 996 " --> pdb=" O GLN c 999 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN c 991 " --> pdb=" O VAL c1029 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 1066 through 1068 Processing sheet with id=AG1, first strand: chain 'd' and resid 933 through 935 removed outlier: 4.086A pdb=" N HIS d 933 " --> pdb=" O VAL d 940 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL d 940 " --> pdb=" O HIS d 933 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU d 935 " --> pdb=" O ARG d 938 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 978 through 980 removed outlier: 3.556A pdb=" N PHE d 979 " --> pdb=" O PHE d1013 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 999 through 1003 removed outlier: 3.834A pdb=" N THR d 996 " --> pdb=" O GLN d 999 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN d 991 " --> pdb=" O VAL d1029 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP d1028 " --> pdb=" O ARG d1036 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG d1036 " --> pdb=" O TRP d1028 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 999 through 1003 removed outlier: 3.834A pdb=" N THR d 996 " --> pdb=" O GLN d 999 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN d 991 " --> pdb=" O VAL d1029 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 1066 through 1068 Processing sheet with id=AG6, first strand: chain 'e' and resid 933 through 935 removed outlier: 3.928A pdb=" N HIS e 933 " --> pdb=" O VAL e 940 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL e 940 " --> pdb=" O HIS e 933 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU e 935 " --> pdb=" O ARG e 938 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'e' and resid 978 through 981 removed outlier: 3.647A pdb=" N LYS e1011 " --> pdb=" O LEU e 981 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'e' and resid 985 through 986 removed outlier: 4.107A pdb=" N THR e 985 " --> pdb=" O ASN e1079 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN e1079 " --> pdb=" O THR e 985 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 999 through 1001 removed outlier: 3.920A pdb=" N THR e 996 " --> pdb=" O GLN e 999 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN e 991 " --> pdb=" O VAL e1029 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA e1024 " --> pdb=" O ASP e1040 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP e1040 " --> pdb=" O ALA e1024 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU e1026 " --> pdb=" O TYR e1038 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP e1028 " --> pdb=" O ARG e1036 " (cutoff:3.500A) 1643 hydrogen bonds defined for protein. 4527 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: 16.13 Time building geometry restraints manager: 17.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17193 1.34 - 1.45: 8019 1.45 - 1.57: 28346 1.57 - 1.69: 2 1.69 - 1.81: 340 Bond restraints: 53900 Sorted by residual: bond pdb=" CA TRP a 848 " pdb=" C TRP a 848 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.48e-02 4.57e+03 8.41e+00 bond pdb=" C LEU e 981 " pdb=" N ARG e 982 " ideal model delta sigma weight residual 1.335 1.256 0.078 3.04e-02 1.08e+03 6.62e+00 bond pdb=" N ARG e 982 " pdb=" CA ARG e 982 " ideal model delta sigma weight residual 1.453 1.416 0.037 1.79e-02 3.12e+03 4.21e+00 bond pdb=" CA TRP d 848 " pdb=" C TRP d 848 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.48e-02 4.57e+03 4.20e+00 bond pdb=" C TYR c 895 " pdb=" N PRO c 896 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.06e+00 ... (remaining 53895 not shown) Histogram of bond angle deviations from ideal: 92.49 - 101.03: 149 101.03 - 109.56: 7166 109.56 - 118.10: 33651 118.10 - 126.63: 31493 126.63 - 135.17: 961 Bond angle restraints: 73420 Sorted by residual: angle pdb=" C GLU e1103 " pdb=" N THR e1104 " pdb=" CA THR e1104 " ideal model delta sigma weight residual 121.31 129.37 -8.06 1.49e+00 4.50e-01 2.92e+01 angle pdb=" N THR e1104 " pdb=" CA THR e1104 " pdb=" C THR e1104 " ideal model delta sigma weight residual 110.35 117.56 -7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" CA THR d 614 " pdb=" CB THR d 614 " pdb=" CG2 THR d 614 " ideal model delta sigma weight residual 110.50 118.11 -7.61 1.70e+00 3.46e-01 2.00e+01 angle pdb=" C PHE c 622 " pdb=" N THR c 623 " pdb=" CA THR c 623 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C PHE e 622 " pdb=" N THR e 623 " pdb=" CA THR e 623 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 73415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 28829 17.56 - 35.11: 2772 35.11 - 52.67: 483 52.67 - 70.22: 79 70.22 - 87.78: 57 Dihedral angle restraints: 32220 sinusoidal: 12400 harmonic: 19820 Sorted by residual: dihedral pdb=" CA ARG b 982 " pdb=" C ARG b 982 " pdb=" N PRO b 983 " pdb=" CA PRO b 983 " ideal model delta harmonic sigma weight residual 180.00 138.41 41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA LEU b 632 " pdb=" C LEU b 632 " pdb=" N PRO b 633 " pdb=" CA PRO b 633 " ideal model delta harmonic sigma weight residual 180.00 139.97 40.03 0 5.00e+00 4.00e-02 6.41e+01 dihedral pdb=" CA LEU c 632 " pdb=" C LEU c 632 " pdb=" N PRO c 633 " pdb=" CA PRO c 633 " ideal model delta harmonic sigma weight residual 180.00 141.55 38.45 0 5.00e+00 4.00e-02 5.91e+01 ... (remaining 32217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 6668 0.062 - 0.124: 1554 0.124 - 0.186: 250 0.186 - 0.248: 27 0.248 - 0.310: 6 Chirality restraints: 8505 Sorted by residual: chirality pdb=" CB ILE b 805 " pdb=" CA ILE b 805 " pdb=" CG1 ILE b 805 " pdb=" CG2 ILE b 805 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE a 805 " pdb=" CA ILE a 805 " pdb=" CG1 ILE a 805 " pdb=" CG2 ILE a 805 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE e 805 " pdb=" CA ILE e 805 " pdb=" CG1 ILE e 805 " pdb=" CG2 ILE e 805 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 8502 not shown) Planarity restraints: 9565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG b 858 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO b 859 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO b 859 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO b 859 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG a 858 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO a 859 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO a 859 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO a 859 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG e 858 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO e 859 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO e 859 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO e 859 " 0.048 5.00e-02 4.00e+02 ... (remaining 9562 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1867 2.70 - 3.25: 49324 3.25 - 3.80: 81740 3.80 - 4.35: 97456 4.35 - 4.90: 159514 Nonbonded interactions: 389901 Sorted by model distance: nonbonded pdb=" OG1 THR A 992 " pdb=" O LEU A1001 " model vdw 2.156 2.440 nonbonded pdb=" OG1 THR B 992 " pdb=" O LEU B1001 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR E 992 " pdb=" O LEU E1001 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR D 992 " pdb=" O LEU D1001 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR C 992 " pdb=" O LEU C1001 " model vdw 2.236 2.440 ... (remaining 389896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'B' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'C' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'D' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'E' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'a' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'b' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'c' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'd' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'e' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 170 5.16 5 C 33345 2.51 5 N 9330 2.21 5 O 10045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.910 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: 0.030 Extract box with map and model: 26.540 Check model and map are aligned: 0.610 Process input model: 100.070 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.380 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.006 0.078 53900 Z= 0.386 Angle : 0.998 14.484 73420 Z= 0.542 Chirality : 0.054 0.310 8505 Planarity : 0.006 0.086 9565 Dihedral : 14.594 87.780 19380 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.08), residues: 6815 helix: -4.05 (0.06), residues: 2360 sheet: -1.64 (0.18), residues: 775 loop : -3.28 (0.08), residues: 3680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1553 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 2 outliers final: 0 residues processed: 1554 average time/residue: 0.5393 time to fit residues: 1361.3596 Evaluate side-chains 1021 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1021 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 578 optimal weight: 0.9990 chunk 519 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 350 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 536 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 326 optimal weight: 0.0470 chunk 399 optimal weight: 0.3980 chunk 622 optimal weight: 0.7980 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 GLN A 687 ASN A 712 GLN A 787 ASN A 804 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS A 999 GLN A1037 GLN A1098 ASN B 687 ASN B 712 GLN B 787 ASN ** B 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 945 ASN B 999 GLN B1071 GLN C 668 GLN C 687 ASN C 712 GLN C 787 ASN C 876 ASN C 999 GLN D 668 GLN D 712 GLN D 787 ASN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 GLN D1098 ASN ** E 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 GLN E 876 ASN E 933 HIS ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS O 118 GLN ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 GLN R 118 GLN ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 820 GLN a 866 GLN a 999 GLN b 593 GLN b 725 GLN ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 812 GLN ** b 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1071 GLN c 593 GLN ** c 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 725 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 812 GLN c 820 GLN c 866 GLN c 991 GLN c1071 GLN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 684 ASN ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 812 GLN d 820 GLN d 866 GLN d 978 HIS d 991 GLN ** e 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 820 GLN e 866 GLN e 991 GLN e 998 ASN e 999 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 53900 Z= 0.217 Angle : 0.685 8.843 73420 Z= 0.352 Chirality : 0.045 0.254 8505 Planarity : 0.005 0.069 9565 Dihedral : 6.142 35.863 7400 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -3.94 (0.09), residues: 6815 helix: -2.90 (0.08), residues: 2360 sheet: -0.76 (0.16), residues: 945 loop : -3.00 (0.09), residues: 3510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1224 time to evaluate : 4.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 1230 average time/residue: 0.5389 time to fit residues: 1104.6886 Evaluate side-chains 972 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 971 time to evaluate : 4.655 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3602 time to fit residues: 7.0750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 345 optimal weight: 0.9980 chunk 193 optimal weight: 0.0270 chunk 517 optimal weight: 0.8980 chunk 423 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 623 optimal weight: 1.9990 chunk 673 optimal weight: 0.9980 chunk 554 optimal weight: 0.7980 chunk 617 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 499 optimal weight: 0.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 999 GLN A1037 GLN A1098 ASN B 668 GLN B 787 ASN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 978 HIS B 999 GLN C 787 ASN C 876 ASN D 787 ASN ** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1032 GLN E 668 GLN E 687 ASN E 787 ASN E 978 HIS E 999 GLN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN H 89 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN J 118 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 GLN Q 53 GLN Q 121 ASN T 53 GLN T 66 GLN a 593 GLN a 812 GLN ** a 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 593 GLN ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 846 GLN ** b 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 999 GLN c 593 GLN c 720 ASN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 593 GLN ** d 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 820 GLN d 927 ASN d 998 ASN d 999 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 803 GLN ** e 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 812 GLN e 991 GLN e 999 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 53900 Z= 0.226 Angle : 0.664 7.489 73420 Z= 0.338 Chirality : 0.044 0.213 8505 Planarity : 0.004 0.065 9565 Dihedral : 5.808 32.755 7400 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -3.44 (0.09), residues: 6815 helix: -2.29 (0.09), residues: 2380 sheet: -0.54 (0.15), residues: 1035 loop : -2.89 (0.10), residues: 3400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1178 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1178 average time/residue: 0.5528 time to fit residues: 1087.3092 Evaluate side-chains 969 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 968 time to evaluate : 4.656 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3829 time to fit residues: 7.1945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 615 optimal weight: 0.2980 chunk 468 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 68 optimal weight: 0.0170 chunk 297 optimal weight: 0.6980 chunk 418 optimal weight: 0.0170 chunk 625 optimal weight: 1.9990 chunk 662 optimal weight: 1.9990 chunk 326 optimal weight: 0.1980 chunk 592 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN C 787 ASN C 876 ASN ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN a 593 GLN a 762 HIS ** a 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 991 GLN a 999 GLN b 866 GLN b 927 ASN c 593 GLN ** c 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 762 HIS ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 593 GLN ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 999 GLN e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 53900 Z= 0.155 Angle : 0.607 10.689 73420 Z= 0.306 Chirality : 0.043 0.202 8505 Planarity : 0.004 0.058 9565 Dihedral : 5.305 32.280 7400 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -3.05 (0.09), residues: 6815 helix: -1.87 (0.10), residues: 2420 sheet: -0.32 (0.16), residues: 1035 loop : -2.74 (0.10), residues: 3360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1176 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1177 average time/residue: 0.5203 time to fit residues: 1020.6879 Evaluate side-chains 960 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 960 time to evaluate : 4.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 551 optimal weight: 0.3980 chunk 375 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 492 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 565 optimal weight: 0.0980 chunk 457 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 594 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN A 862 GLN A 978 HIS B 787 ASN B 804 GLN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 933 HIS B 978 HIS B 991 GLN B 999 GLN C 787 ASN C 804 GLN C 876 ASN D 787 ASN ** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 991 GLN E 998 ASN H 121 ASN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN Q 121 ASN T 66 GLN a 593 GLN ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 927 ASN ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 593 GLN c 640 ASN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 846 GLN d 593 GLN ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 812 GLN d 820 GLN ** d 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 53900 Z= 0.240 Angle : 0.672 8.553 73420 Z= 0.338 Chirality : 0.045 0.272 8505 Planarity : 0.004 0.070 9565 Dihedral : 5.453 31.549 7400 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.10), residues: 6815 helix: -1.62 (0.10), residues: 2430 sheet: -0.41 (0.15), residues: 1065 loop : -2.64 (0.10), residues: 3320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1114 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 1115 average time/residue: 0.5125 time to fit residues: 958.7652 Evaluate side-chains 945 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 943 time to evaluate : 4.663 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3640 time to fit residues: 7.7382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 222 optimal weight: 0.0010 chunk 596 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 662 optimal weight: 0.9990 chunk 550 optimal weight: 0.8980 chunk 306 optimal weight: 0.0000 chunk 55 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 999 GLN C 787 ASN C 876 ASN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 ASN E 820 GLN E 824 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 927 ASN a 933 HIS ** b 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN c 593 GLN c 725 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 876 ASN d 593 GLN ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 999 GLN e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 933 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 53900 Z= 0.170 Angle : 0.612 9.531 73420 Z= 0.308 Chirality : 0.043 0.289 8505 Planarity : 0.004 0.065 9565 Dihedral : 5.155 30.434 7400 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.09), residues: 6815 helix: -1.40 (0.10), residues: 2510 sheet: -0.28 (0.18), residues: 810 loop : -2.61 (0.10), residues: 3495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1126 time to evaluate : 4.705 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: 3 outliers final: 2 residues processed: 1129 average time/residue: 0.5210 time to fit residues: 984.9866 Evaluate side-chains 951 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 949 time to evaluate : 4.786 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4126 time to fit residues: 7.9529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 638 optimal weight: 2.9990 chunk 74 optimal weight: 0.0370 chunk 377 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 374 optimal weight: 0.8980 chunk 557 optimal weight: 0.2980 chunk 370 optimal weight: 3.9990 chunk 660 optimal weight: 0.8980 chunk 413 optimal weight: 0.0170 chunk 402 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 999 GLN C 787 ASN C 876 ASN D 876 ASN E 787 ASN E 824 GLN G 53 GLN H 121 ASN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN T 27 HIS T 66 GLN a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 927 ASN b 762 HIS ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 593 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 876 ASN c1079 ASN d 593 GLN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 846 GLN e 593 GLN e 625 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 53900 Z= 0.166 Angle : 0.613 9.201 73420 Z= 0.307 Chirality : 0.043 0.314 8505 Planarity : 0.004 0.054 9565 Dihedral : 4.991 27.894 7400 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 6815 helix: -1.21 (0.10), residues: 2510 sheet: -0.29 (0.17), residues: 810 loop : -2.54 (0.10), residues: 3495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1102 time to evaluate : 4.584 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: 3 outliers final: 2 residues processed: 1103 average time/residue: 0.5317 time to fit residues: 988.1084 Evaluate side-chains 952 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 950 time to evaluate : 4.723 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3754 time to fit residues: 7.9146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 408 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 394 optimal weight: 0.0050 chunk 198 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 419 optimal weight: 3.9990 chunk 449 optimal weight: 0.9980 chunk 326 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 518 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 999 GLN C 787 ASN C 876 ASN C1037 GLN ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN b 999 GLN c 593 GLN c 725 GLN c 789 GLN c 803 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 593 GLN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 53900 Z= 0.179 Angle : 0.627 12.001 73420 Z= 0.311 Chirality : 0.043 0.229 8505 Planarity : 0.004 0.080 9565 Dihedral : 4.942 26.231 7400 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.10), residues: 6815 helix: -1.10 (0.10), residues: 2515 sheet: -0.43 (0.16), residues: 945 loop : -2.54 (0.10), residues: 3355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1098 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1099 average time/residue: 0.5174 time to fit residues: 955.4186 Evaluate side-chains 951 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 951 time to evaluate : 4.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 600 optimal weight: 0.8980 chunk 632 optimal weight: 8.9990 chunk 577 optimal weight: 0.3980 chunk 615 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 483 optimal weight: 0.0370 chunk 188 optimal weight: 10.0000 chunk 555 optimal weight: 0.9980 chunk 581 optimal weight: 0.0970 chunk 613 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 999 GLN C 787 ASN C 876 ASN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 HIS H 121 ASN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN ** T 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 803 GLN ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 846 GLN a 853 GLN a 999 GLN ** b 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 762 HIS b 803 GLN ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN b 999 GLN c 593 GLN c 789 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 593 GLN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 803 GLN ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 978 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 53900 Z= 0.175 Angle : 0.636 13.431 73420 Z= 0.313 Chirality : 0.044 0.191 8505 Planarity : 0.004 0.081 9565 Dihedral : 4.883 26.400 7400 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 6815 helix: -0.99 (0.10), residues: 2515 sheet: -0.41 (0.16), residues: 945 loop : -2.51 (0.10), residues: 3355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1090 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 1091 average time/residue: 0.5169 time to fit residues: 947.9034 Evaluate side-chains 945 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 943 time to evaluate : 4.767 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3775 time to fit residues: 8.0087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 404 optimal weight: 6.9990 chunk 650 optimal weight: 2.9990 chunk 397 optimal weight: 0.0870 chunk 308 optimal weight: 4.9990 chunk 452 optimal weight: 0.7980 chunk 682 optimal weight: 1.9990 chunk 628 optimal weight: 1.9990 chunk 543 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 419 optimal weight: 0.5980 chunk 333 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 933 HIS B 999 GLN C 787 ASN C 876 ASN D 846 GLN D 876 ASN D 991 GLN D1032 GLN D1037 GLN ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 978 HIS ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 GLN K 66 GLN K 121 ASN ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN a 593 GLN a 803 GLN ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 927 ASN ** b 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN c 593 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1079 ASN d 593 GLN ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1071 GLN e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 803 GLN ** e 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 978 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 53900 Z= 0.217 Angle : 0.665 14.465 73420 Z= 0.330 Chirality : 0.044 0.175 8505 Planarity : 0.004 0.082 9565 Dihedral : 5.046 25.930 7400 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.10), residues: 6815 helix: -1.00 (0.10), residues: 2520 sheet: -0.52 (0.16), residues: 900 loop : -2.48 (0.10), residues: 3395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1079 time to evaluate : 4.727 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: 4 outliers final: 1 residues processed: 1081 average time/residue: 0.5142 time to fit residues: 934.0966 Evaluate side-chains 935 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 934 time to evaluate : 4.682 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3666 time to fit residues: 7.1026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 431 optimal weight: 0.3980 chunk 578 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 501 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 544 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 558 optimal weight: 0.2980 chunk 68 optimal weight: 0.0060 chunk 100 optimal weight: 5.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 999 GLN C 787 ASN C 876 ASN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN H 121 ASN K 66 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 GLN Q 121 ASN a 592 HIS a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 803 GLN ** a 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 687 ASN ** b 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 927 ASN c 593 GLN ** c 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 593 GLN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 593 GLN e 725 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.134288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115494 restraints weight = 108062.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115568 restraints weight = 109104.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115638 restraints weight = 102187.353| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 53900 Z= 0.159 Angle : 0.635 14.172 73420 Z= 0.311 Chirality : 0.043 0.180 8505 Planarity : 0.004 0.077 9565 Dihedral : 4.818 27.314 7400 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 6815 helix: -0.87 (0.10), residues: 2520 sheet: -0.37 (0.16), residues: 915 loop : -2.43 (0.10), residues: 3380 =============================================================================== Job complete usr+sys time: 13984.71 seconds wall clock time: 244 minutes 3.47 seconds (14643.47 seconds total)