Starting phenix.real_space_refine on Sat Mar 16 21:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jan_36130/03_2024/8jan_36130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jan_36130/03_2024/8jan_36130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jan_36130/03_2024/8jan_36130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jan_36130/03_2024/8jan_36130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jan_36130/03_2024/8jan_36130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jan_36130/03_2024/8jan_36130.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 47466 2.51 5 N 12594 2.21 5 O 14742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "g GLU 87": "OE1" <-> "OE2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "j GLU 87": "OE1" <-> "OE2" Residue "k TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 60": "OE1" <-> "OE2" Residue "n GLU 191": "OE1" <-> "OE2" Residue "o GLU 219": "OE1" <-> "OE2" Residue "p GLU 191": "OE1" <-> "OE2" Residue "s GLU 502": "OE1" <-> "OE2" Residue "u GLU 492": "OE1" <-> "OE2" Residue "y GLU 42": "OE1" <-> "OE2" Residue "y PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "D GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 75114 Number of models: 1 Model: "" Number of chains: 30 Chain: "a" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1304 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "b" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1304 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "c" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1304 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "d" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1304 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "e" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1304 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "f" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1304 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "g" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "h" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "i" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "j" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "k" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3984 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 499} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "n" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3984 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 499} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "o" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3984 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 499} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "p" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3984 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 499} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "q" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3984 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 499} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "r" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3984 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 499} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3975 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "t" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3975 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "u" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3975 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "v" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3975 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "w" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3975 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "x" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3975 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "y" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2020 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "z" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2020 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2020 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2020 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2020 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2020 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 28.59, per 1000 atoms: 0.38 Number of scatterers: 75114 At special positions: 0 Unit cell: (208.08, 216.24, 179.52, 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 312 16.00 O 14742 8.00 N 12594 7.00 C 47466 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: 22.77 Conformation dependent library (CDL) restraints added in 10.4 seconds 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18252 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 115 sheets defined 23.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'a' and resid 9 through 23 removed outlier: 3.983A pdb=" N ILE a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS a 23 " --> pdb=" O ALA a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 44 removed outlier: 4.051A pdb=" N ILE a 42 " --> pdb=" O HIS a 39 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER a 43 " --> pdb=" O GLU a 40 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL a 44 " --> pdb=" O ASP a 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 39 through 44' Processing helix chain 'a' and resid 91 through 103 Processing helix chain 'b' and resid 9 through 23 removed outlier: 3.873A pdb=" N ILE b 13 " --> pdb=" O ASN b 9 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS b 23 " --> pdb=" O ALA b 19 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 44 No H-bonds generated for 'chain 'b' and resid 42 through 44' Processing helix chain 'b' and resid 91 through 103 Processing helix chain 'b' and resid 127 through 131 removed outlier: 3.568A pdb=" N THR b 131 " --> pdb=" O ALA b 128 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 23 removed outlier: 3.967A pdb=" N ILE c 13 " --> pdb=" O ASN c 9 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS c 23 " --> pdb=" O ALA c 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 44 No H-bonds generated for 'chain 'c' and resid 42 through 44' Processing helix chain 'c' and resid 91 through 103 Processing helix chain 'd' and resid 9 through 23 removed outlier: 3.920A pdb=" N ILE d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS d 23 " --> pdb=" O ALA d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 44 No H-bonds generated for 'chain 'd' and resid 42 through 44' Processing helix chain 'd' and resid 91 through 103 Processing helix chain 'e' and resid 9 through 23 removed outlier: 3.874A pdb=" N ILE e 13 " --> pdb=" O ASN e 9 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS e 23 " --> pdb=" O ALA e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 44 No H-bonds generated for 'chain 'e' and resid 42 through 44' Processing helix chain 'e' and resid 91 through 103 Processing helix chain 'f' and resid 9 through 23 removed outlier: 3.962A pdb=" N ILE f 13 " --> pdb=" O ASN f 9 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS f 23 " --> pdb=" O ALA f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 44 No H-bonds generated for 'chain 'f' and resid 42 through 44' Processing helix chain 'f' and resid 91 through 103 Processing helix chain 'g' and resid 39 through 44 removed outlier: 3.567A pdb=" N ILE g 42 " --> pdb=" O HIS g 39 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL g 44 " --> pdb=" O ASP g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 103 Processing helix chain 'g' and resid 124 through 129 Processing helix chain 'h' and resid 39 through 44 removed outlier: 3.719A pdb=" N ILE h 42 " --> pdb=" O HIS h 39 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL h 44 " --> pdb=" O ASP h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 91 through 103 Processing helix chain 'h' and resid 124 through 129 Processing helix chain 'i' and resid 39 through 44 removed outlier: 3.720A pdb=" N ILE i 42 " --> pdb=" O HIS i 39 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL i 44 " --> pdb=" O ASP i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 103 Processing helix chain 'i' and resid 124 through 129 Processing helix chain 'j' and resid 39 through 44 removed outlier: 3.571A pdb=" N ILE j 42 " --> pdb=" O HIS j 39 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL j 44 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 103 Processing helix chain 'j' and resid 124 through 130 Processing helix chain 'k' and resid 39 through 44 removed outlier: 3.719A pdb=" N ILE k 42 " --> pdb=" O HIS k 39 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL k 44 " --> pdb=" O ASP k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 Processing helix chain 'k' and resid 124 through 129 Processing helix chain 'l' and resid 39 through 44 removed outlier: 3.663A pdb=" N ILE l 42 " --> pdb=" O HIS l 39 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL l 44 " --> pdb=" O ASP l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 103 Processing helix chain 'l' and resid 124 through 129 Processing helix chain 'm' and resid 59 through 65 Processing helix chain 'm' and resid 76 through 87 removed outlier: 3.769A pdb=" N ARG m 80 " --> pdb=" O PHE m 76 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN m 87 " --> pdb=" O TYR m 83 " (cutoff:3.500A) Processing helix chain 'm' and resid 201 through 210 Processing helix chain 'm' and resid 221 through 225 removed outlier: 4.225A pdb=" N ALA m 225 " --> pdb=" O ILE m 222 " (cutoff:3.500A) Processing helix chain 'm' and resid 247 through 260 removed outlier: 3.755A pdb=" N TYR m 251 " --> pdb=" O SER m 247 " (cutoff:3.500A) Processing helix chain 'm' and resid 275 through 290 Processing helix chain 'm' and resid 302 through 313 removed outlier: 4.105A pdb=" N LEU m 307 " --> pdb=" O TYR m 303 " (cutoff:3.500A) Proline residue: m 308 - end of helix removed outlier: 3.684A pdb=" N GLU m 311 " --> pdb=" O LEU m 307 " (cutoff:3.500A) Processing helix chain 'm' and resid 345 through 358 removed outlier: 3.545A pdb=" N ALA m 349 " --> pdb=" O LEU m 345 " (cutoff:3.500A) Processing helix chain 'm' and resid 393 through 400 Processing helix chain 'm' and resid 431 through 451 removed outlier: 3.508A pdb=" N MET m 451 " --> pdb=" O LEU m 447 " (cutoff:3.500A) Processing helix chain 'm' and resid 458 through 477 Processing helix chain 'n' and resid 59 through 65 Processing helix chain 'n' and resid 76 through 87 removed outlier: 3.724A pdb=" N ARG n 80 " --> pdb=" O PHE n 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN n 87 " --> pdb=" O TYR n 83 " (cutoff:3.500A) Processing helix chain 'n' and resid 201 through 210 Processing helix chain 'n' and resid 221 through 225 removed outlier: 4.218A pdb=" N ALA n 225 " --> pdb=" O ILE n 222 " (cutoff:3.500A) Processing helix chain 'n' and resid 247 through 260 removed outlier: 3.771A pdb=" N TYR n 251 " --> pdb=" O SER n 247 " (cutoff:3.500A) Processing helix chain 'n' and resid 275 through 290 Processing helix chain 'n' and resid 302 through 314 removed outlier: 4.165A pdb=" N LEU n 307 " --> pdb=" O TYR n 303 " (cutoff:3.500A) Proline residue: n 308 - end of helix removed outlier: 3.708A pdb=" N GLU n 311 " --> pdb=" O LEU n 307 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY n 314 " --> pdb=" O VAL n 310 " (cutoff:3.500A) Processing helix chain 'n' and resid 345 through 358 Processing helix chain 'n' and resid 393 through 400 Processing helix chain 'n' and resid 431 through 451 removed outlier: 3.618A pdb=" N MET n 451 " --> pdb=" O LEU n 447 " (cutoff:3.500A) Processing helix chain 'n' and resid 458 through 477 Processing helix chain 'o' and resid 59 through 65 Processing helix chain 'o' and resid 76 through 87 removed outlier: 3.703A pdb=" N ARG o 80 " --> pdb=" O PHE o 76 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN o 87 " --> pdb=" O TYR o 83 " (cutoff:3.500A) Processing helix chain 'o' and resid 201 through 210 removed outlier: 3.533A pdb=" N SER o 210 " --> pdb=" O LEU o 206 " (cutoff:3.500A) Processing helix chain 'o' and resid 221 through 225 removed outlier: 4.155A pdb=" N ALA o 225 " --> pdb=" O ILE o 222 " (cutoff:3.500A) Processing helix chain 'o' and resid 247 through 260 removed outlier: 3.794A pdb=" N TYR o 251 " --> pdb=" O SER o 247 " (cutoff:3.500A) Processing helix chain 'o' and resid 275 through 290 Processing helix chain 'o' and resid 302 through 314 removed outlier: 4.252A pdb=" N LEU o 307 " --> pdb=" O TYR o 303 " (cutoff:3.500A) Proline residue: o 308 - end of helix removed outlier: 3.740A pdb=" N GLU o 311 " --> pdb=" O LEU o 307 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY o 314 " --> pdb=" O VAL o 310 " (cutoff:3.500A) Processing helix chain 'o' and resid 345 through 358 removed outlier: 3.644A pdb=" N ALA o 349 " --> pdb=" O LEU o 345 " (cutoff:3.500A) Processing helix chain 'o' and resid 393 through 400 Processing helix chain 'o' and resid 431 through 451 removed outlier: 3.519A pdb=" N MET o 451 " --> pdb=" O LEU o 447 " (cutoff:3.500A) Processing helix chain 'o' and resid 458 through 478 removed outlier: 3.516A pdb=" N GLY o 478 " --> pdb=" O PHE o 474 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 65 Processing helix chain 'p' and resid 76 through 87 removed outlier: 3.769A pdb=" N ARG p 80 " --> pdb=" O PHE p 76 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN p 87 " --> pdb=" O TYR p 83 " (cutoff:3.500A) Processing helix chain 'p' and resid 201 through 210 Processing helix chain 'p' and resid 221 through 225 removed outlier: 4.220A pdb=" N ALA p 225 " --> pdb=" O ILE p 222 " (cutoff:3.500A) Processing helix chain 'p' and resid 247 through 260 removed outlier: 3.780A pdb=" N TYR p 251 " --> pdb=" O SER p 247 " (cutoff:3.500A) Processing helix chain 'p' and resid 275 through 290 Processing helix chain 'p' and resid 302 through 313 removed outlier: 4.105A pdb=" N LEU p 307 " --> pdb=" O TYR p 303 " (cutoff:3.500A) Proline residue: p 308 - end of helix removed outlier: 3.682A pdb=" N GLU p 311 " --> pdb=" O LEU p 307 " (cutoff:3.500A) Processing helix chain 'p' and resid 345 through 358 removed outlier: 3.547A pdb=" N ALA p 349 " --> pdb=" O LEU p 345 " (cutoff:3.500A) Processing helix chain 'p' and resid 393 through 400 Processing helix chain 'p' and resid 431 through 451 removed outlier: 3.507A pdb=" N MET p 451 " --> pdb=" O LEU p 447 " (cutoff:3.500A) Processing helix chain 'p' and resid 458 through 477 Processing helix chain 'q' and resid 59 through 65 Processing helix chain 'q' and resid 76 through 87 removed outlier: 3.724A pdb=" N ARG q 80 " --> pdb=" O PHE q 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN q 87 " --> pdb=" O TYR q 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 201 through 210 Processing helix chain 'q' and resid 221 through 225 removed outlier: 4.218A pdb=" N ALA q 225 " --> pdb=" O ILE q 222 " (cutoff:3.500A) Processing helix chain 'q' and resid 247 through 260 removed outlier: 3.771A pdb=" N TYR q 251 " --> pdb=" O SER q 247 " (cutoff:3.500A) Processing helix chain 'q' and resid 275 through 290 Processing helix chain 'q' and resid 302 through 314 removed outlier: 4.157A pdb=" N LEU q 307 " --> pdb=" O TYR q 303 " (cutoff:3.500A) Proline residue: q 308 - end of helix removed outlier: 3.720A pdb=" N GLU q 311 " --> pdb=" O LEU q 307 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY q 314 " --> pdb=" O VAL q 310 " (cutoff:3.500A) Processing helix chain 'q' and resid 345 through 358 Processing helix chain 'q' and resid 393 through 400 Processing helix chain 'q' and resid 431 through 451 removed outlier: 3.645A pdb=" N MET q 451 " --> pdb=" O LEU q 447 " (cutoff:3.500A) Processing helix chain 'q' and resid 458 through 477 Processing helix chain 'r' and resid 59 through 65 Processing helix chain 'r' and resid 76 through 87 removed outlier: 3.709A pdb=" N ARG r 80 " --> pdb=" O PHE r 76 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN r 87 " --> pdb=" O TYR r 83 " (cutoff:3.500A) Processing helix chain 'r' and resid 201 through 210 removed outlier: 3.510A pdb=" N SER r 210 " --> pdb=" O LEU r 206 " (cutoff:3.500A) Processing helix chain 'r' and resid 221 through 225 removed outlier: 4.163A pdb=" N ALA r 225 " --> pdb=" O ILE r 222 " (cutoff:3.500A) Processing helix chain 'r' and resid 247 through 260 removed outlier: 3.785A pdb=" N TYR r 251 " --> pdb=" O SER r 247 " (cutoff:3.500A) Processing helix chain 'r' and resid 275 through 290 Processing helix chain 'r' and resid 302 through 314 removed outlier: 4.238A pdb=" N LEU r 307 " --> pdb=" O TYR r 303 " (cutoff:3.500A) Proline residue: r 308 - end of helix removed outlier: 3.742A pdb=" N GLU r 311 " --> pdb=" O LEU r 307 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY r 314 " --> pdb=" O VAL r 310 " (cutoff:3.500A) Processing helix chain 'r' and resid 345 through 358 removed outlier: 3.643A pdb=" N ALA r 349 " --> pdb=" O LEU r 345 " (cutoff:3.500A) Processing helix chain 'r' and resid 393 through 401 Processing helix chain 'r' and resid 431 through 451 removed outlier: 3.537A pdb=" N MET r 451 " --> pdb=" O LEU r 447 " (cutoff:3.500A) Processing helix chain 'r' and resid 458 through 477 Processing helix chain 's' and resid 76 through 86 removed outlier: 3.558A pdb=" N ARG s 80 " --> pdb=" O PHE s 76 " (cutoff:3.500A) Processing helix chain 's' and resid 201 through 210 Processing helix chain 's' and resid 247 through 260 removed outlier: 3.645A pdb=" N TYR s 251 " --> pdb=" O SER s 247 " (cutoff:3.500A) Processing helix chain 's' and resid 275 through 289 Processing helix chain 's' and resid 302 through 313 removed outlier: 4.077A pdb=" N LEU s 307 " --> pdb=" O TYR s 303 " (cutoff:3.500A) Proline residue: s 308 - end of helix removed outlier: 3.552A pdb=" N GLU s 311 " --> pdb=" O LEU s 307 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR s 313 " --> pdb=" O ALA s 309 " (cutoff:3.500A) Processing helix chain 's' and resid 348 through 358 Processing helix chain 's' and resid 393 through 400 Processing helix chain 's' and resid 431 through 451 removed outlier: 3.675A pdb=" N SER s 435 " --> pdb=" O GLN s 431 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET s 437 " --> pdb=" O VAL s 433 " (cutoff:3.500A) Processing helix chain 's' and resid 459 through 477 removed outlier: 3.805A pdb=" N LYS s 465 " --> pdb=" O ALA s 461 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY s 466 " --> pdb=" O GLY s 462 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET s 467 " --> pdb=" O LEU s 463 " (cutoff:3.500A) Processing helix chain 't' and resid 76 through 86 removed outlier: 3.543A pdb=" N ARG t 80 " --> pdb=" O PHE t 76 " (cutoff:3.500A) Processing helix chain 't' and resid 201 through 210 Processing helix chain 't' and resid 247 through 260 removed outlier: 3.635A pdb=" N TYR t 251 " --> pdb=" O SER t 247 " (cutoff:3.500A) Processing helix chain 't' and resid 275 through 289 Processing helix chain 't' and resid 302 through 313 removed outlier: 4.016A pdb=" N LEU t 307 " --> pdb=" O TYR t 303 " (cutoff:3.500A) Proline residue: t 308 - end of helix removed outlier: 3.540A pdb=" N GLU t 311 " --> pdb=" O LEU t 307 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR t 313 " --> pdb=" O ALA t 309 " (cutoff:3.500A) Processing helix chain 't' and resid 347 through 358 Processing helix chain 't' and resid 393 through 400 Processing helix chain 't' and resid 431 through 453 removed outlier: 3.649A pdb=" N SER t 435 " --> pdb=" O GLN t 431 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET t 437 " --> pdb=" O VAL t 433 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N HIS t 453 " --> pdb=" O ARG t 449 " (cutoff:3.500A) Processing helix chain 't' and resid 461 through 478 removed outlier: 3.808A pdb=" N LYS t 465 " --> pdb=" O ALA t 461 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY t 466 " --> pdb=" O GLY t 462 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET t 467 " --> pdb=" O LEU t 463 " (cutoff:3.500A) Processing helix chain 'u' and resid 76 through 87 removed outlier: 3.542A pdb=" N ARG u 80 " --> pdb=" O PHE u 76 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN u 87 " --> pdb=" O TYR u 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 201 through 210 Processing helix chain 'u' and resid 247 through 260 removed outlier: 3.685A pdb=" N TYR u 251 " --> pdb=" O SER u 247 " (cutoff:3.500A) Processing helix chain 'u' and resid 275 through 289 Processing helix chain 'u' and resid 302 through 313 removed outlier: 4.088A pdb=" N LEU u 307 " --> pdb=" O TYR u 303 " (cutoff:3.500A) Proline residue: u 308 - end of helix removed outlier: 3.572A pdb=" N GLU u 311 " --> pdb=" O LEU u 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR u 313 " --> pdb=" O ALA u 309 " (cutoff:3.500A) Processing helix chain 'u' and resid 348 through 358 Processing helix chain 'u' and resid 393 through 400 Processing helix chain 'u' and resid 431 through 452 removed outlier: 3.648A pdb=" N SER u 435 " --> pdb=" O GLN u 431 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET u 437 " --> pdb=" O VAL u 433 " (cutoff:3.500A) Processing helix chain 'u' and resid 459 through 478 removed outlier: 3.512A pdb=" N THR u 464 " --> pdb=" O ALA u 460 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS u 465 " --> pdb=" O ALA u 461 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY u 466 " --> pdb=" O GLY u 462 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 86 removed outlier: 3.562A pdb=" N ARG v 80 " --> pdb=" O PHE v 76 " (cutoff:3.500A) Processing helix chain 'v' and resid 201 through 210 Processing helix chain 'v' and resid 247 through 260 removed outlier: 3.646A pdb=" N TYR v 251 " --> pdb=" O SER v 247 " (cutoff:3.500A) Processing helix chain 'v' and resid 275 through 289 Processing helix chain 'v' and resid 302 through 313 removed outlier: 4.074A pdb=" N LEU v 307 " --> pdb=" O TYR v 303 " (cutoff:3.500A) Proline residue: v 308 - end of helix removed outlier: 3.551A pdb=" N GLU v 311 " --> pdb=" O LEU v 307 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR v 313 " --> pdb=" O ALA v 309 " (cutoff:3.500A) Processing helix chain 'v' and resid 348 through 358 Processing helix chain 'v' and resid 393 through 400 Processing helix chain 'v' and resid 431 through 452 removed outlier: 3.681A pdb=" N SER v 435 " --> pdb=" O GLN v 431 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET v 437 " --> pdb=" O VAL v 433 " (cutoff:3.500A) Processing helix chain 'v' and resid 461 through 477 removed outlier: 3.843A pdb=" N LYS v 465 " --> pdb=" O ALA v 461 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY v 466 " --> pdb=" O GLY v 462 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET v 467 " --> pdb=" O LEU v 463 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 86 removed outlier: 3.543A pdb=" N ARG w 80 " --> pdb=" O PHE w 76 " (cutoff:3.500A) Processing helix chain 'w' and resid 201 through 210 Processing helix chain 'w' and resid 247 through 260 removed outlier: 3.615A pdb=" N TYR w 251 " --> pdb=" O SER w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 275 through 289 Processing helix chain 'w' and resid 302 through 313 removed outlier: 4.018A pdb=" N LEU w 307 " --> pdb=" O TYR w 303 " (cutoff:3.500A) Proline residue: w 308 - end of helix removed outlier: 3.546A pdb=" N GLU w 311 " --> pdb=" O LEU w 307 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR w 313 " --> pdb=" O ALA w 309 " (cutoff:3.500A) Processing helix chain 'w' and resid 347 through 358 Processing helix chain 'w' and resid 393 through 400 Processing helix chain 'w' and resid 431 through 452 removed outlier: 3.632A pdb=" N SER w 435 " --> pdb=" O GLN w 431 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET w 437 " --> pdb=" O VAL w 433 " (cutoff:3.500A) Processing helix chain 'w' and resid 461 through 478 removed outlier: 3.737A pdb=" N LYS w 465 " --> pdb=" O ALA w 461 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY w 466 " --> pdb=" O GLY w 462 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET w 467 " --> pdb=" O LEU w 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 76 through 87 removed outlier: 3.545A pdb=" N ARG x 80 " --> pdb=" O PHE x 76 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN x 87 " --> pdb=" O TYR x 83 " (cutoff:3.500A) Processing helix chain 'x' and resid 201 through 210 Processing helix chain 'x' and resid 247 through 260 removed outlier: 3.670A pdb=" N TYR x 251 " --> pdb=" O SER x 247 " (cutoff:3.500A) Processing helix chain 'x' and resid 275 through 289 Processing helix chain 'x' and resid 302 through 313 removed outlier: 4.086A pdb=" N LEU x 307 " --> pdb=" O TYR x 303 " (cutoff:3.500A) Proline residue: x 308 - end of helix removed outlier: 3.574A pdb=" N GLU x 311 " --> pdb=" O LEU x 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR x 313 " --> pdb=" O ALA x 309 " (cutoff:3.500A) Processing helix chain 'x' and resid 348 through 358 Processing helix chain 'x' and resid 393 through 400 Processing helix chain 'x' and resid 431 through 452 removed outlier: 3.652A pdb=" N SER x 435 " --> pdb=" O GLN x 431 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET x 437 " --> pdb=" O VAL x 433 " (cutoff:3.500A) Processing helix chain 'x' and resid 462 through 478 removed outlier: 3.887A pdb=" N GLY x 466 " --> pdb=" O GLY x 462 " (cutoff:3.500A) Processing helix chain 'y' and resid 29 through 45 removed outlier: 4.351A pdb=" N ASP y 33 " --> pdb=" O ILE y 29 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER y 34 " --> pdb=" O ASP y 30 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU y 42 " --> pdb=" O GLN y 38 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA y 43 " --> pdb=" O ALA y 39 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE y 44 " --> pdb=" O LEU y 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 65 Processing helix chain 'y' and resid 66 through 70 Processing helix chain 'y' and resid 78 through 89 Processing helix chain 'y' and resid 163 through 180 removed outlier: 3.796A pdb=" N LEU y 167 " --> pdb=" O GLU y 163 " (cutoff:3.500A) Processing helix chain 'z' and resid 29 through 45 removed outlier: 4.381A pdb=" N ASP z 33 " --> pdb=" O ILE z 29 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER z 34 " --> pdb=" O ASP z 30 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN z 41 " --> pdb=" O ALA z 37 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU z 42 " --> pdb=" O GLN z 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA z 43 " --> pdb=" O ALA z 39 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE z 44 " --> pdb=" O LEU z 40 " (cutoff:3.500A) Processing helix chain 'z' and resid 56 through 65 Processing helix chain 'z' and resid 66 through 70 Processing helix chain 'z' and resid 78 through 89 Processing helix chain 'z' and resid 163 through 180 removed outlier: 3.754A pdb=" N LEU z 167 " --> pdb=" O GLU z 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.320A pdb=" N ASP A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 78 through 89 Processing helix chain 'A' and resid 163 through 180 removed outlier: 3.747A pdb=" N LEU A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.332A pdb=" N ASP B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 163 through 180 removed outlier: 3.794A pdb=" N LEU B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 45 removed outlier: 4.155A pdb=" N SER C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 65 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 163 through 180 removed outlier: 3.769A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 4.330A pdb=" N ASP D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 65 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 78 through 89 Processing helix chain 'D' and resid 163 through 180 removed outlier: 3.745A pdb=" N LEU D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 33 through 34 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 33 through 34 current: chain 'a' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 79 through 85 current: chain 'a' and resid 132 through 140 Processing sheet with id=AA2, first strand: chain 'a' and resid 56 through 62 removed outlier: 4.652A pdb=" N GLU a 57 " --> pdb=" O GLY a 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'a' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 144 through 147 current: chain 'b' and resid 81 through 85 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 81 through 85 current: chain 'b' and resid 132 through 141 Processing sheet with id=AA5, first strand: chain 'b' and resid 56 through 62 removed outlier: 5.390A pdb=" N VAL b 59 " --> pdb=" O HIS b 72 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS b 72 " --> pdb=" O VAL b 59 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP b 61 " --> pdb=" O ASN b 70 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN b 70 " --> pdb=" O ASP b 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'b' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 144 through 147 current: chain 'c' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 79 through 85 current: chain 'c' and resid 132 through 141 Processing sheet with id=AA8, first strand: chain 'c' and resid 56 through 62 removed outlier: 5.376A pdb=" N VAL c 59 " --> pdb=" O HIS c 72 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS c 72 " --> pdb=" O VAL c 59 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP c 61 " --> pdb=" O ASN c 70 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN c 70 " --> pdb=" O ASP c 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'c' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 144 through 147 current: chain 'd' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 79 through 85 current: chain 'd' and resid 132 through 140 Processing sheet with id=AB2, first strand: chain 'd' and resid 56 through 62 removed outlier: 4.651A pdb=" N GLU d 57 " --> pdb=" O GLY d 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 119 through 120 Processing sheet with id=AB4, first strand: chain 'd' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 144 through 147 current: chain 'e' and resid 81 through 85 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 81 through 85 current: chain 'e' and resid 131 through 141 Processing sheet with id=AB5, first strand: chain 'e' and resid 56 through 62 removed outlier: 5.359A pdb=" N VAL e 59 " --> pdb=" O HIS e 72 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS e 72 " --> pdb=" O VAL e 59 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP e 61 " --> pdb=" O ASN e 70 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN e 70 " --> pdb=" O ASP e 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'e' and resid 119 through 120 Processing sheet with id=AB7, first strand: chain 'e' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 144 through 147 current: chain 'f' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 79 through 85 current: chain 'f' and resid 132 through 140 Processing sheet with id=AB8, first strand: chain 'f' and resid 56 through 62 removed outlier: 5.392A pdb=" N VAL f 59 " --> pdb=" O HIS f 72 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS f 72 " --> pdb=" O VAL f 59 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP f 61 " --> pdb=" O ASN f 70 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN f 70 " --> pdb=" O ASP f 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 119 through 120 Processing sheet with id=AC1, first strand: chain 'g' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 17 through 19 current: chain 'x' and resid 505 through 512 WARNING: can't find start of bonding for strands! previous: chain 'x' and resid 505 through 512 current: chain 'D' and resid 7 through 26 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 7 through 26 current: chain 'D' and resid 109 through 114 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 109 through 114 current: chain 'D' and resid 142 through 161 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 142 through 161 current: chain 'D' and resid 198 through 206 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 198 through 206 current: chain 'D' and resid 227 through 258 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'g' and resid 33 through 34 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 33 through 34 current: chain 'g' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 79 through 85 current: chain 'g' and resid 132 through 141 Processing sheet with id=AC3, first strand: chain 'g' and resid 56 through 62 removed outlier: 4.709A pdb=" N GLU g 57 " --> pdb=" O GLY g 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 144 through 147 current: chain 'h' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 79 through 85 current: chain 'h' and resid 132 through 141 Processing sheet with id=AC5, first strand: chain 'h' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 17 through 19 current: chain 's' and resid 505 through 512 WARNING: can't find start of bonding for strands! previous: chain 's' and resid 505 through 512 current: chain 'y' and resid 7 through 26 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 7 through 26 current: chain 'y' and resid 109 through 114 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 109 through 114 current: chain 'y' and resid 142 through 161 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 142 through 161 current: chain 'y' and resid 198 through 206 WARNING: can't find start of bonding for strands! previous: chain 'y' and resid 198 through 206 current: chain 'y' and resid 227 through 258 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'h' and resid 56 through 62 removed outlier: 4.683A pdb=" N GLU h 57 " --> pdb=" O GLY h 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 144 through 147 current: chain 'i' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 79 through 85 current: chain 'i' and resid 132 through 141 Processing sheet with id=AC8, first strand: chain 'i' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 17 through 19 current: chain 't' and resid 505 through 512 WARNING: can't find start of bonding for strands! previous: chain 't' and resid 505 through 512 current: chain 'z' and resid 7 through 26 WARNING: can't find start of bonding for strands! previous: chain 'z' and resid 7 through 26 current: chain 'z' and resid 109 through 114 WARNING: can't find start of bonding for strands! previous: chain 'z' and resid 109 through 114 current: chain 'z' and resid 142 through 161 WARNING: can't find start of bonding for strands! previous: chain 'z' and resid 142 through 161 current: chain 'z' and resid 198 through 206 WARNING: can't find start of bonding for strands! previous: chain 'z' and resid 198 through 206 current: chain 'z' and resid 227 through 258 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'i' and resid 56 through 62 removed outlier: 4.715A pdb=" N GLU i 57 " --> pdb=" O GLY i 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'i' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 144 through 147 current: chain 'j' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 79 through 85 current: chain 'j' and resid 131 through 141 Processing sheet with id=AD2, first strand: chain 'j' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 16 through 19 current: chain 'u' and resid 505 through 512 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 505 through 512 current: chain 'A' and resid 7 through 26 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 7 through 26 current: chain 'A' and resid 109 through 114 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 114 current: chain 'A' and resid 141 through 161 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 141 through 161 current: chain 'A' and resid 198 through 206 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 198 through 206 current: chain 'A' and resid 227 through 258 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'j' and resid 56 through 62 removed outlier: 4.716A pdb=" N GLU j 57 " --> pdb=" O GLY j 73 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 144 through 147 current: chain 'k' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 79 through 85 current: chain 'k' and resid 132 through 141 Processing sheet with id=AD5, first strand: chain 'k' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 17 through 19 current: chain 'v' and resid 505 through 512 WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 505 through 512 current: chain 'B' and resid 7 through 26 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 7 through 26 current: chain 'B' and resid 109 through 114 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 109 through 114 current: chain 'B' and resid 142 through 161 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 142 through 161 current: chain 'B' and resid 198 through 206 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 198 through 206 current: chain 'B' and resid 227 through 258 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'k' and resid 56 through 62 removed outlier: 4.688A pdb=" N GLU k 57 " --> pdb=" O GLY k 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 144 through 147 current: chain 'l' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 79 through 85 current: chain 'l' and resid 132 through 141 Processing sheet with id=AD8, first strand: chain 'l' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 17 through 19 current: chain 'w' and resid 505 through 512 WARNING: can't find start of bonding for strands! previous: chain 'w' and resid 505 through 512 current: chain 'C' and resid 7 through 26 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 7 through 26 current: chain 'C' and resid 109 through 114 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 109 through 114 current: chain 'C' and resid 144 through 161 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 144 through 161 current: chain 'C' and resid 198 through 206 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 198 through 206 current: chain 'C' and resid 227 through 258 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'l' and resid 56 through 62 removed outlier: 4.715A pdb=" N GLU l 57 " --> pdb=" O GLY l 73 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'm' and resid 16 through 18 removed outlier: 6.259A pdb=" N ALA m 17 " --> pdb=" O GLY n 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'm' and resid 38 through 42 removed outlier: 6.343A pdb=" N TRP m 38 " --> pdb=" O TYR m 92 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL m 94 " --> pdb=" O TRP m 38 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY m 40 " --> pdb=" O VAL m 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 115 through 120 removed outlier: 3.506A pdb=" N VAL m 137 " --> pdb=" O PRO m 104 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE m 133 " --> pdb=" O PHE m 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'm' and resid 178 through 187 removed outlier: 6.679A pdb=" N LEU m 169 " --> pdb=" O LEU m 181 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR m 183 " --> pdb=" O LEU m 167 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU m 167 " --> pdb=" O THR m 183 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR m 185 " --> pdb=" O PHE m 165 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE m 165 " --> pdb=" O THR m 185 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ARG m 148 " --> pdb=" O ALA m 234 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA m 234 " --> pdb=" O ARG m 148 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU m 150 " --> pdb=" O SER m 232 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'm' and resid 267 through 269 removed outlier: 6.423A pdb=" N VAL m 268 " --> pdb=" O PHE m 294 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASP m 296 " --> pdb=" O VAL m 268 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'm' and resid 340 through 341 Processing sheet with id=AE7, first strand: chain 'm' and resid 377 through 378 removed outlier: 4.076A pdb=" N MET m 413 " --> pdb=" O ILE m 378 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'm' and resid 494 through 502 removed outlier: 6.625A pdb=" N LYS m 505 " --> pdb=" O ALA m 501 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS m 512 " --> pdb=" O LEU s 526 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'm' and resid 521 through 523 Processing sheet with id=AF1, first strand: chain 'n' and resid 16 through 18 removed outlier: 6.182A pdb=" N ALA n 17 " --> pdb=" O GLY o 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'n' and resid 38 through 42 removed outlier: 6.303A pdb=" N TRP n 38 " --> pdb=" O TYR n 92 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N VAL n 94 " --> pdb=" O TRP n 38 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY n 40 " --> pdb=" O VAL n 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'n' and resid 115 through 120 removed outlier: 3.511A pdb=" N VAL n 137 " --> pdb=" O PRO n 104 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'n' and resid 178 through 187 removed outlier: 6.687A pdb=" N LEU n 169 " --> pdb=" O LEU n 181 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR n 183 " --> pdb=" O LEU n 167 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU n 167 " --> pdb=" O THR n 183 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR n 185 " --> pdb=" O PHE n 165 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE n 165 " --> pdb=" O THR n 185 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE n 152 " --> pdb=" O LYS n 231 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS n 231 " --> pdb=" O ILE n 152 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'n' and resid 267 through 269 removed outlier: 6.540A pdb=" N VAL n 268 " --> pdb=" O PHE n 294 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP n 296 " --> pdb=" O VAL n 268 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'n' and resid 340 through 341 Processing sheet with id=AF7, first strand: chain 'n' and resid 405 through 407 Processing sheet with id=AF8, first strand: chain 'n' and resid 494 through 502 removed outlier: 3.577A pdb=" N ALA n 501 " --> pdb=" O LYS n 505 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS n 505 " --> pdb=" O ALA n 501 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA s 17 " --> pdb=" O GLY t 523 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'o' and resid 16 through 18 removed outlier: 6.372A pdb=" N ALA o 17 " --> pdb=" O GLY p 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'o' and resid 52 through 55 removed outlier: 6.292A pdb=" N TRP o 38 " --> pdb=" O TYR o 92 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL o 94 " --> pdb=" O TRP o 38 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY o 40 " --> pdb=" O VAL o 94 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA o 39 " --> pdb=" O LEU o 269 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL o 268 " --> pdb=" O PHE o 294 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASP o 296 " --> pdb=" O VAL o 268 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'o' and resid 115 through 120 Processing sheet with id=AG3, first strand: chain 'o' and resid 178 through 187 removed outlier: 6.761A pdb=" N LEU o 169 " --> pdb=" O LEU o 181 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR o 183 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU o 167 " --> pdb=" O THR o 183 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR o 185 " --> pdb=" O PHE o 165 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE o 165 " --> pdb=" O THR o 185 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE o 152 " --> pdb=" O LYS o 231 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS o 231 " --> pdb=" O ILE o 152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'o' and resid 340 through 341 Processing sheet with id=AG5, first strand: chain 'o' and resid 377 through 378 removed outlier: 4.050A pdb=" N MET o 413 " --> pdb=" O ILE o 378 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'o' and resid 494 through 502 removed outlier: 6.593A pdb=" N LYS o 505 " --> pdb=" O ALA o 501 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP o 506 " --> pdb=" O GLN u 522 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL u 524 " --> pdb=" O TRP o 506 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL o 508 " --> pdb=" O VAL u 524 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU u 526 " --> pdb=" O VAL o 508 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP o 510 " --> pdb=" O LEU u 526 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA t 17 " --> pdb=" O GLY u 523 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'p' and resid 16 through 18 removed outlier: 6.256A pdb=" N ALA p 17 " --> pdb=" O GLY q 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'p' and resid 38 through 42 removed outlier: 6.376A pdb=" N TRP p 38 " --> pdb=" O TYR p 92 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL p 94 " --> pdb=" O TRP p 38 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY p 40 " --> pdb=" O VAL p 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'p' and resid 115 through 120 removed outlier: 3.504A pdb=" N VAL p 137 " --> pdb=" O PRO p 104 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'p' and resid 178 through 187 removed outlier: 6.679A pdb=" N LEU p 169 " --> pdb=" O LEU p 181 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR p 183 " --> pdb=" O LEU p 167 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU p 167 " --> pdb=" O THR p 183 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR p 185 " --> pdb=" O PHE p 165 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE p 165 " --> pdb=" O THR p 185 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE p 152 " --> pdb=" O LYS p 231 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS p 231 " --> pdb=" O ILE p 152 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'p' and resid 267 through 269 removed outlier: 6.460A pdb=" N VAL p 268 " --> pdb=" O PHE p 294 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASP p 296 " --> pdb=" O VAL p 268 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 340 through 341 Processing sheet with id=AH4, first strand: chain 'p' and resid 377 through 378 removed outlier: 4.079A pdb=" N MET p 413 " --> pdb=" O ILE p 378 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'p' and resid 494 through 502 removed outlier: 6.612A pdb=" N LYS p 505 " --> pdb=" O ALA p 501 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY u 15 " --> pdb=" O ILE v 521 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLY v 523 " --> pdb=" O GLY u 15 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA u 17 " --> pdb=" O GLY v 523 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 16 through 18 removed outlier: 6.252A pdb=" N ALA q 17 " --> pdb=" O GLY r 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'q' and resid 38 through 42 removed outlier: 6.289A pdb=" N TRP q 38 " --> pdb=" O TYR q 92 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N VAL q 94 " --> pdb=" O TRP q 38 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY q 40 " --> pdb=" O VAL q 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 115 through 120 removed outlier: 3.511A pdb=" N VAL q 137 " --> pdb=" O PRO q 104 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'q' and resid 178 through 187 removed outlier: 6.672A pdb=" N LEU q 169 " --> pdb=" O LEU q 181 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR q 183 " --> pdb=" O LEU q 167 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU q 167 " --> pdb=" O THR q 183 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR q 185 " --> pdb=" O PHE q 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE q 165 " --> pdb=" O THR q 185 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE q 152 " --> pdb=" O LYS q 231 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS q 231 " --> pdb=" O ILE q 152 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'q' and resid 267 through 269 removed outlier: 6.521A pdb=" N VAL q 268 " --> pdb=" O PHE q 294 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP q 296 " --> pdb=" O VAL q 268 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q' and resid 340 through 341 Processing sheet with id=AI3, first strand: chain 'q' and resid 405 through 407 Processing sheet with id=AI4, first strand: chain 'q' and resid 494 through 502 removed outlier: 3.583A pdb=" N ALA q 501 " --> pdb=" O LYS q 505 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS q 505 " --> pdb=" O ALA q 501 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP q 510 " --> pdb=" O VAL w 524 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA v 17 " --> pdb=" O GLY w 523 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'r' and resid 52 through 55 removed outlier: 6.292A pdb=" N TRP r 38 " --> pdb=" O TYR r 92 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL r 94 " --> pdb=" O TRP r 38 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY r 40 " --> pdb=" O VAL r 94 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA r 39 " --> pdb=" O LEU r 269 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL r 268 " --> pdb=" O PHE r 294 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ASP r 296 " --> pdb=" O VAL r 268 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'r' and resid 115 through 120 Processing sheet with id=AI7, first strand: chain 'r' and resid 178 through 187 removed outlier: 6.753A pdb=" N LEU r 169 " --> pdb=" O LEU r 181 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR r 183 " --> pdb=" O LEU r 167 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU r 167 " --> pdb=" O THR r 183 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR r 185 " --> pdb=" O PHE r 165 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE r 165 " --> pdb=" O THR r 185 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE r 152 " --> pdb=" O LYS r 231 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS r 231 " --> pdb=" O ILE r 152 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'r' and resid 340 through 341 Processing sheet with id=AI9, first strand: chain 'r' and resid 377 through 378 removed outlier: 4.044A pdb=" N MET r 413 " --> pdb=" O ILE r 378 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 494 through 502 removed outlier: 3.507A pdb=" N ALA r 511 " --> pdb=" O VAL r 495 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU r 507 " --> pdb=" O THR r 499 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS r 505 " --> pdb=" O ALA r 501 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP r 506 " --> pdb=" O GLN x 522 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL x 524 " --> pdb=" O TRP r 506 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL r 508 " --> pdb=" O VAL x 524 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU x 526 " --> pdb=" O VAL r 508 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP r 510 " --> pdb=" O LEU x 526 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA w 17 " --> pdb=" O GLY x 523 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 's' and resid 38 through 42 removed outlier: 6.455A pdb=" N TRP s 38 " --> pdb=" O TYR s 92 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N VAL s 94 " --> pdb=" O TRP s 38 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY s 40 " --> pdb=" O VAL s 94 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 's' and resid 114 through 120 removed outlier: 3.762A pdb=" N VAL s 137 " --> pdb=" O PRO s 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE s 133 " --> pdb=" O PHE s 108 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 's' and resid 178 through 187 removed outlier: 5.267A pdb=" N THR s 180 " --> pdb=" O GLN s 171 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN s 171 " --> pdb=" O THR s 180 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE s 152 " --> pdb=" O LYS s 231 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS s 231 " --> pdb=" O ILE s 152 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 's' and resid 267 through 269 removed outlier: 6.530A pdb=" N VAL s 268 " --> pdb=" O PHE s 294 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASP s 296 " --> pdb=" O VAL s 268 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 's' and resid 330 through 331 Processing sheet with id=AJ7, first strand: chain 's' and resid 405 through 407 Processing sheet with id=AJ8, first strand: chain 't' and resid 52 through 55 removed outlier: 6.188A pdb=" N TRP t 38 " --> pdb=" O TYR t 92 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL t 94 " --> pdb=" O TRP t 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY t 40 " --> pdb=" O VAL t 94 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA t 39 " --> pdb=" O LEU t 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL t 268 " --> pdb=" O PHE t 294 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASP t 296 " --> pdb=" O VAL t 268 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 't' and resid 114 through 120 removed outlier: 3.698A pdb=" N VAL t 137 " --> pdb=" O PRO t 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE t 133 " --> pdb=" O PHE t 108 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 't' and resid 178 through 186 removed outlier: 5.378A pdb=" N THR t 180 " --> pdb=" O GLN t 171 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN t 171 " --> pdb=" O THR t 180 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU t 182 " --> pdb=" O LEU t 169 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE t 152 " --> pdb=" O LYS t 231 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS t 231 " --> pdb=" O ILE t 152 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 't' and resid 330 through 331 Processing sheet with id=AK3, first strand: chain 't' and resid 405 through 407 Processing sheet with id=AK4, first strand: chain 'u' and resid 38 through 42 removed outlier: 6.369A pdb=" N TRP u 38 " --> pdb=" O TYR u 92 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL u 94 " --> pdb=" O TRP u 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY u 40 " --> pdb=" O VAL u 94 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'u' and resid 114 through 120 removed outlier: 3.686A pdb=" N VAL u 137 " --> pdb=" O PRO u 104 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE u 133 " --> pdb=" O PHE u 108 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'u' and resid 178 through 186 removed outlier: 6.647A pdb=" N LEU u 169 " --> pdb=" O LEU u 181 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR u 183 " --> pdb=" O LEU u 167 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU u 167 " --> pdb=" O THR u 183 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR u 185 " --> pdb=" O PHE u 165 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE u 165 " --> pdb=" O THR u 185 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE u 152 " --> pdb=" O LYS u 231 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS u 231 " --> pdb=" O ILE u 152 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'u' and resid 267 through 269 removed outlier: 6.538A pdb=" N VAL u 268 " --> pdb=" O PHE u 294 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ASP u 296 " --> pdb=" O VAL u 268 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'u' and resid 330 through 331 Processing sheet with id=AK9, first strand: chain 'u' and resid 405 through 407 Processing sheet with id=AL1, first strand: chain 'v' and resid 38 through 42 Processing sheet with id=AL2, first strand: chain 'v' and resid 114 through 120 removed outlier: 3.757A pdb=" N VAL v 137 " --> pdb=" O PRO v 104 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE v 133 " --> pdb=" O PHE v 108 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'v' and resid 178 through 187 removed outlier: 5.275A pdb=" N THR v 180 " --> pdb=" O GLN v 171 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN v 171 " --> pdb=" O THR v 180 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE v 152 " --> pdb=" O LYS v 231 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS v 231 " --> pdb=" O ILE v 152 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'v' and resid 267 through 269 removed outlier: 6.534A pdb=" N VAL v 268 " --> pdb=" O PHE v 294 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ASP v 296 " --> pdb=" O VAL v 268 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'v' and resid 330 through 331 Processing sheet with id=AL6, first strand: chain 'v' and resid 405 through 407 Processing sheet with id=AL7, first strand: chain 'w' and resid 52 through 55 removed outlier: 6.176A pdb=" N TRP w 38 " --> pdb=" O TYR w 92 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL w 94 " --> pdb=" O TRP w 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY w 40 " --> pdb=" O VAL w 94 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA w 39 " --> pdb=" O LEU w 269 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL w 268 " --> pdb=" O PHE w 294 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASP w 296 " --> pdb=" O VAL w 268 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'w' and resid 114 through 120 removed outlier: 3.703A pdb=" N VAL w 137 " --> pdb=" O PRO w 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE w 133 " --> pdb=" O PHE w 108 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'w' and resid 178 through 186 removed outlier: 5.364A pdb=" N THR w 180 " --> pdb=" O GLN w 171 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLN w 171 " --> pdb=" O THR w 180 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG w 148 " --> pdb=" O ALA w 234 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA w 234 " --> pdb=" O ARG w 148 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU w 150 " --> pdb=" O SER w 232 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER w 232 " --> pdb=" O LEU w 150 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'w' and resid 330 through 331 Processing sheet with id=AM2, first strand: chain 'w' and resid 405 through 407 Processing sheet with id=AM3, first strand: chain 'x' and resid 52 through 55 removed outlier: 6.219A pdb=" N TRP x 38 " --> pdb=" O TYR x 92 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL x 94 " --> pdb=" O TRP x 38 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY x 40 " --> pdb=" O VAL x 94 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA x 39 " --> pdb=" O LEU x 269 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL x 268 " --> pdb=" O PHE x 294 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ASP x 296 " --> pdb=" O VAL x 268 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'x' and resid 114 through 120 removed outlier: 3.684A pdb=" N VAL x 137 " --> pdb=" O PRO x 104 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE x 133 " --> pdb=" O PHE x 108 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'x' and resid 178 through 186 removed outlier: 5.312A pdb=" N THR x 180 " --> pdb=" O GLN x 171 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN x 171 " --> pdb=" O THR x 180 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE x 152 " --> pdb=" O LYS x 231 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS x 231 " --> pdb=" O ILE x 152 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'x' and resid 330 through 331 Processing sheet with id=AM7, first strand: chain 'x' and resid 405 through 407 1981 hydrogen bonds defined for protein. 5745 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: 30.81 Time building geometry restraints manager: 25.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 12922 1.31 - 1.44: 19613 1.44 - 1.56: 43581 1.56 - 1.69: 0 1.69 - 1.82: 468 Bond restraints: 76584 Sorted by residual: bond pdb=" C ASP C 33 " pdb=" O ASP C 33 " ideal model delta sigma weight residual 1.237 1.189 0.047 1.16e-02 7.43e+03 1.67e+01 bond pdb=" C ASP z 33 " pdb=" O ASP z 33 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.62e+01 bond pdb=" N ASP z 33 " pdb=" CA ASP z 33 " ideal model delta sigma weight residual 1.459 1.415 0.044 1.20e-02 6.94e+03 1.37e+01 bond pdb=" N ASP C 33 " pdb=" CA ASP C 33 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.20e-02 6.94e+03 1.29e+01 bond pdb=" CA ASP C 33 " pdb=" C ASP C 33 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.26e-02 6.30e+03 8.60e+00 ... (remaining 76579 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.25: 1857 106.25 - 113.22: 42049 113.22 - 120.19: 26006 120.19 - 127.16: 33499 127.16 - 134.13: 725 Bond angle restraints: 104136 Sorted by residual: angle pdb=" C GLU x 502 " pdb=" CA GLU x 502 " pdb=" CB GLU x 502 " ideal model delta sigma weight residual 115.89 110.60 5.29 1.32e+00 5.74e-01 1.61e+01 angle pdb=" C LYS x 452 " pdb=" N HIS x 453 " pdb=" CA HIS x 453 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.36e+01 angle pdb=" CB MET v 467 " pdb=" CG MET v 467 " pdb=" SD MET v 467 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" CB MET s 467 " pdb=" CG MET s 467 " pdb=" SD MET s 467 " ideal model delta sigma weight residual 112.70 121.82 -9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" C THR c 148 " pdb=" N GLU c 149 " pdb=" CA GLU c 149 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.40e+00 ... (remaining 104131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 42137 17.89 - 35.77: 3232 35.77 - 53.66: 441 53.66 - 71.55: 65 71.55 - 89.44: 49 Dihedral angle restraints: 45924 sinusoidal: 17502 harmonic: 28422 Sorted by residual: dihedral pdb=" CA LYS j 118 " pdb=" C LYS j 118 " pdb=" N SER j 119 " pdb=" CA SER j 119 " ideal model delta harmonic sigma weight residual 180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU k 34 " pdb=" C LEU k 34 " pdb=" N THR k 35 " pdb=" CA THR k 35 " ideal model delta harmonic sigma weight residual 180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU h 34 " pdb=" C LEU h 34 " pdb=" N THR h 35 " pdb=" CA THR h 35 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 45921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 8247 0.036 - 0.072: 2405 0.072 - 0.109: 922 0.109 - 0.145: 423 0.145 - 0.181: 15 Chirality restraints: 12012 Sorted by residual: chirality pdb=" CB THR n 224 " pdb=" CA THR n 224 " pdb=" OG1 THR n 224 " pdb=" CG2 THR n 224 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CB THR q 224 " pdb=" CA THR q 224 " pdb=" OG1 THR q 224 " pdb=" CG2 THR q 224 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB THR o 224 " pdb=" CA THR o 224 " pdb=" OG1 THR o 224 " pdb=" CG2 THR o 224 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 12009 not shown) Planarity restraints: 13488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER s 454 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO s 455 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO s 455 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO s 455 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL o 524 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO o 525 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO o 525 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO o 525 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL s 97 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO s 98 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO s 98 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO s 98 " 0.023 5.00e-02 4.00e+02 ... (remaining 13485 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5969 2.74 - 3.28: 69941 3.28 - 3.82: 112742 3.82 - 4.36: 131952 4.36 - 4.90: 244047 Nonbonded interactions: 564651 Sorted by model distance: nonbonded pdb=" O VAL m 310 " pdb=" OG1 THR m 313 " model vdw 2.199 2.440 nonbonded pdb=" O VAL p 310 " pdb=" OG1 THR p 313 " model vdw 2.202 2.440 nonbonded pdb=" O VAL n 310 " pdb=" OG1 THR n 313 " model vdw 2.203 2.440 nonbonded pdb=" O VAL o 310 " pdb=" OG1 THR o 313 " model vdw 2.205 2.440 nonbonded pdb=" O VAL q 310 " pdb=" OG1 THR q 313 " model vdw 2.205 2.440 ... (remaining 564646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'a' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 168)) selection = (chain 'b' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 168)) selection = (chain 'c' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 168)) selection = (chain 'd' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 168)) selection = (chain 'e' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 168)) selection = (chain 'f' and ((resid 11 and (name N or name CA or name C or name O or name CB \ )) or resid 12 through 168)) selection = (chain 'g' and resid 11 through 168) selection = (chain 'h' and resid 11 through 168) selection = (chain 'i' and resid 11 through 168) selection = (chain 'j' and resid 11 through 168) selection = (chain 'k' and resid 11 through 168) selection = (chain 'l' and resid 11 through 168) } ncs_group { reference = (chain 'm' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 528)) selection = (chain 'n' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 528)) selection = (chain 'o' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 528)) selection = (chain 'p' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 528)) selection = (chain 'q' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 528)) selection = (chain 'r' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 528)) selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.380 Check model and map are aligned: 0.850 Set scattering table: 0.510 Process input model: 153.710 Find NCS groups from input model: 4.390 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 76584 Z= 0.218 Angle : 0.531 9.228 104136 Z= 0.283 Chirality : 0.044 0.181 12012 Planarity : 0.004 0.058 13488 Dihedral : 12.829 89.437 27672 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.08), residues: 9774 helix: 1.44 (0.11), residues: 2202 sheet: 0.95 (0.11), residues: 2100 loop : -1.38 (0.07), residues: 5472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 506 HIS 0.005 0.001 HIS s 429 PHE 0.022 0.001 PHE i 36 TYR 0.020 0.001 TYR q 201 ARG 0.008 0.000 ARG g 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 6.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 186 VAL cc_start: 0.8883 (t) cc_final: 0.8677 (t) REVERT: r 506 TRP cc_start: 0.6295 (m100) cc_final: 0.5285 (m100) REVERT: u 451 MET cc_start: 0.8992 (tpp) cc_final: 0.8634 (tpp) REVERT: v 196 MET cc_start: 0.8814 (mtt) cc_final: 0.8553 (mtt) REVERT: x 186 VAL cc_start: 0.9080 (t) cc_final: 0.8870 (m) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.6912 time to fit residues: 399.4592 Evaluate side-chains 303 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 6.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 815 optimal weight: 8.9990 chunk 732 optimal weight: 10.0000 chunk 406 optimal weight: 0.9980 chunk 250 optimal weight: 0.0770 chunk 493 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 757 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 460 optimal weight: 9.9990 chunk 563 optimal weight: 0.3980 chunk 877 optimal weight: 2.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 184 HIS ** m 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 184 HIS p 184 HIS q 184 HIS r 34 ASN r 184 HIS ** r 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 76584 Z= 0.126 Angle : 0.460 6.831 104136 Z= 0.238 Chirality : 0.042 0.163 12012 Planarity : 0.003 0.040 13488 Dihedral : 4.026 22.856 10590 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.28 % Allowed : 3.84 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.08), residues: 9774 helix: 1.63 (0.11), residues: 2196 sheet: 0.96 (0.12), residues: 2004 loop : -1.26 (0.07), residues: 5574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP w 510 HIS 0.005 0.001 HIS q 429 PHE 0.012 0.001 PHE o 343 TYR 0.013 0.001 TYR q 201 ARG 0.006 0.000 ARG g 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 344 time to evaluate : 6.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 127 LYS cc_start: 0.8949 (tptp) cc_final: 0.8326 (tppt) REVERT: p 264 MET cc_start: 0.7915 (tmm) cc_final: 0.7530 (ttp) outliers start: 23 outliers final: 14 residues processed: 353 average time/residue: 0.6995 time to fit residues: 428.2065 Evaluate side-chains 318 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 304 time to evaluate : 6.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 489 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 487 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 730 optimal weight: 0.3980 chunk 597 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 878 optimal weight: 0.0270 chunk 949 optimal weight: 10.0000 chunk 782 optimal weight: 0.4980 chunk 871 optimal weight: 20.0000 chunk 299 optimal weight: 0.9980 chunk 705 optimal weight: 10.0000 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 ASN e 5 ASN ** m 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 500 GLN u 453 HIS ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 76584 Z= 0.127 Angle : 0.436 6.724 104136 Z= 0.226 Chirality : 0.042 0.160 12012 Planarity : 0.003 0.040 13488 Dihedral : 3.834 21.962 10590 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.33 % Allowed : 5.75 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.08), residues: 9774 helix: 1.78 (0.12), residues: 2196 sheet: 1.00 (0.12), residues: 1980 loop : -1.23 (0.07), residues: 5598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP r 506 HIS 0.005 0.001 HIS u 453 PHE 0.013 0.001 PHE o 343 TYR 0.011 0.001 TYR p 350 ARG 0.005 0.000 ARG g 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 323 time to evaluate : 6.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 155 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8638 (p) REVERT: i 127 LYS cc_start: 0.8935 (tptp) cc_final: 0.8329 (tppt) REVERT: k 155 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8644 (p) REVERT: l 127 LYS cc_start: 0.8945 (tptp) cc_final: 0.8583 (tppt) REVERT: s 186 VAL cc_start: 0.8876 (t) cc_final: 0.8660 (t) REVERT: v 470 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8657 (mp) outliers start: 27 outliers final: 13 residues processed: 337 average time/residue: 0.7173 time to fit residues: 416.3828 Evaluate side-chains 313 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 297 time to evaluate : 6.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain h residue 155 VAL Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain k residue 155 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain v residue 470 LEU Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 489 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 868 optimal weight: 9.9990 chunk 660 optimal weight: 0.7980 chunk 456 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 419 optimal weight: 5.9990 chunk 590 optimal weight: 10.0000 chunk 881 optimal weight: 20.0000 chunk 933 optimal weight: 10.0000 chunk 460 optimal weight: 3.9990 chunk 835 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 65 ASN ** m 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 500 GLN u 453 HIS ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 76584 Z= 0.190 Angle : 0.469 6.562 104136 Z= 0.244 Chirality : 0.043 0.172 12012 Planarity : 0.003 0.040 13488 Dihedral : 4.036 24.181 10590 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.62 % Allowed : 6.87 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.08), residues: 9774 helix: 1.76 (0.12), residues: 2196 sheet: 0.98 (0.11), residues: 2124 loop : -1.32 (0.07), residues: 5454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP t 506 HIS 0.005 0.001 HIS a 72 PHE 0.013 0.001 PHE r 343 TYR 0.013 0.001 TYR o 350 ARG 0.006 0.000 ARG g 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 6.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 127 LYS cc_start: 0.8966 (tptp) cc_final: 0.8707 (tptm) REVERT: k 155 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8706 (p) REVERT: n 429 HIS cc_start: 0.7295 (m170) cc_final: 0.6996 (m90) REVERT: p 264 MET cc_start: 0.7935 (tmm) cc_final: 0.7300 (ttp) REVERT: v 470 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8628 (mp) outliers start: 50 outliers final: 21 residues processed: 335 average time/residue: 0.7127 time to fit residues: 413.3995 Evaluate side-chains 313 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 290 time to evaluate : 6.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 11 LYS Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain k residue 155 VAL Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 145 ASP Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain v residue 470 LEU Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain A residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 777 optimal weight: 8.9990 chunk 530 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 695 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 796 optimal weight: 5.9990 chunk 645 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 476 optimal weight: 3.9990 chunk 838 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 65 ASN m 426 ASN ** r 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 453 HIS ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 76584 Z= 0.263 Angle : 0.517 6.923 104136 Z= 0.271 Chirality : 0.044 0.179 12012 Planarity : 0.004 0.047 13488 Dihedral : 4.387 24.191 10590 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.78 % Allowed : 8.20 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.08), residues: 9774 helix: 1.59 (0.11), residues: 2190 sheet: 0.90 (0.11), residues: 2148 loop : -1.40 (0.07), residues: 5436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP w 510 HIS 0.006 0.001 HIS k 72 PHE 0.017 0.002 PHE o 343 TYR 0.015 0.001 TYR o 350 ARG 0.007 0.000 ARG g 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 303 time to evaluate : 6.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: k 155 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8795 (p) REVERT: l 127 LYS cc_start: 0.9012 (tptp) cc_final: 0.8650 (tppt) REVERT: n 429 HIS cc_start: 0.7385 (m170) cc_final: 0.7106 (m90) REVERT: p 107 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: p 264 MET cc_start: 0.7956 (tmm) cc_final: 0.7327 (ttp) REVERT: q 506 TRP cc_start: 0.7407 (m100) cc_final: 0.7206 (m100) REVERT: r 436 LEU cc_start: 0.8296 (mt) cc_final: 0.8056 (mt) outliers start: 63 outliers final: 31 residues processed: 344 average time/residue: 0.7044 time to fit residues: 419.1696 Evaluate side-chains 326 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 6.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 11 LYS Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain k residue 155 VAL Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain m residue 107 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 524 VAL Chi-restraints excluded: chain p residue 107 MET Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 506 TRP Chi-restraints excluded: chain r residue 508 VAL Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain x residue 504 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 314 optimal weight: 5.9990 chunk 840 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 548 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 934 optimal weight: 9.9990 chunk 775 optimal weight: 10.0000 chunk 432 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 490 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 20 ASN g 65 ASN j 20 ASN j 65 ASN ** m 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 453 HIS ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 76584 Z= 0.490 Angle : 0.651 8.898 104136 Z= 0.345 Chirality : 0.049 0.198 12012 Planarity : 0.005 0.059 13488 Dihedral : 5.053 26.644 10590 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.93 % Allowed : 9.13 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.08), residues: 9774 helix: 1.19 (0.11), residues: 2178 sheet: 0.51 (0.12), residues: 2022 loop : -1.66 (0.07), residues: 5574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP t 510 HIS 0.009 0.002 HIS h 72 PHE 0.018 0.002 PHE d 12 TYR 0.021 0.002 TYR r 427 ARG 0.008 0.001 ARG r 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 302 time to evaluate : 6.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: j 94 LEU cc_start: 0.8831 (mm) cc_final: 0.8499 (mt) REVERT: m 264 MET cc_start: 0.7962 (tmm) cc_final: 0.7432 (ttp) REVERT: p 264 MET cc_start: 0.7998 (tmm) cc_final: 0.7423 (ttp) REVERT: s 46 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8210 (ptt-90) REVERT: s 297 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8259 (t) REVERT: v 46 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8215 (ptt-90) outliers start: 75 outliers final: 51 residues processed: 355 average time/residue: 0.6995 time to fit residues: 429.8460 Evaluate side-chains 338 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 284 time to evaluate : 7.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 86 VAL Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 125 VAL Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain j residue 118 LYS Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 145 ASP Chi-restraints excluded: chain m residue 222 ILE Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain n residue 508 VAL Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 105 ILE Chi-restraints excluded: chain o residue 508 VAL Chi-restraints excluded: chain o residue 524 VAL Chi-restraints excluded: chain p residue 186 VAL Chi-restraints excluded: chain p residue 222 ILE Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 239 THR Chi-restraints excluded: chain q residue 508 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 100 ASP Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 506 TRP Chi-restraints excluded: chain r residue 508 VAL Chi-restraints excluded: chain r residue 524 VAL Chi-restraints excluded: chain s residue 46 ARG Chi-restraints excluded: chain s residue 268 VAL Chi-restraints excluded: chain s residue 297 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain t residue 504 ASP Chi-restraints excluded: chain u residue 62 ASP Chi-restraints excluded: chain u residue 321 VAL Chi-restraints excluded: chain v residue 46 ARG Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 268 VAL Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain x residue 504 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 901 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 532 optimal weight: 3.9990 chunk 682 optimal weight: 9.9990 chunk 528 optimal weight: 2.9990 chunk 786 optimal weight: 2.9990 chunk 521 optimal weight: 9.9990 chunk 931 optimal weight: 2.9990 chunk 582 optimal weight: 10.0000 chunk 567 optimal weight: 2.9990 chunk 429 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 246 GLN C 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 76584 Z= 0.233 Angle : 0.509 7.016 104136 Z= 0.268 Chirality : 0.044 0.180 12012 Planarity : 0.004 0.059 13488 Dihedral : 4.648 25.492 10590 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.87 % Allowed : 9.76 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.08), residues: 9774 helix: 1.38 (0.11), residues: 2184 sheet: 0.54 (0.12), residues: 2034 loop : -1.59 (0.07), residues: 5556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP q 506 HIS 0.008 0.001 HIS q 429 PHE 0.017 0.001 PHE o 343 TYR 0.013 0.001 TYR o 350 ARG 0.005 0.000 ARG g 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 302 time to evaluate : 6.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: j 111 MET cc_start: 0.8794 (tpt) cc_final: 0.7906 (tpt) REVERT: m 264 MET cc_start: 0.7904 (tmm) cc_final: 0.7381 (ttp) REVERT: p 264 MET cc_start: 0.7969 (tmm) cc_final: 0.7424 (ttp) REVERT: s 46 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8335 (ptt-90) REVERT: t 125 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8188 (tp) REVERT: v 46 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8333 (ptt-90) REVERT: w 125 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8178 (tp) REVERT: A 246 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7774 (tp-100) REVERT: D 246 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7731 (tp-100) outliers start: 70 outliers final: 51 residues processed: 350 average time/residue: 0.7112 time to fit residues: 429.9910 Evaluate side-chains 341 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 286 time to evaluate : 6.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain b residue 86 VAL Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 11 LYS Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain j residue 118 LYS Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain l residue 145 ASP Chi-restraints excluded: chain m residue 222 ILE Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain n residue 508 VAL Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 105 ILE Chi-restraints excluded: chain o residue 508 VAL Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 239 THR Chi-restraints excluded: chain q residue 508 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 100 ASP Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 500 GLN Chi-restraints excluded: chain r residue 506 TRP Chi-restraints excluded: chain r residue 508 VAL Chi-restraints excluded: chain s residue 46 ARG Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 268 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 125 ILE Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain t residue 504 ASP Chi-restraints excluded: chain v residue 46 ARG Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 268 VAL Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 125 ILE Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain x residue 504 ASP Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain D residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 576 optimal weight: 9.9990 chunk 371 optimal weight: 6.9990 chunk 556 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 591 optimal weight: 10.0000 chunk 634 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 731 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 76584 Z= 0.325 Angle : 0.552 7.195 104136 Z= 0.291 Chirality : 0.045 0.186 12012 Planarity : 0.004 0.061 13488 Dihedral : 4.756 25.166 10590 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.94 % Allowed : 10.07 % Favored : 88.99 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 9774 helix: 1.35 (0.11), residues: 2184 sheet: 0.49 (0.12), residues: 2022 loop : -1.67 (0.07), residues: 5568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP q 506 HIS 0.007 0.002 HIS q 429 PHE 0.017 0.002 PHE o 343 TYR 0.016 0.001 TYR o 350 ARG 0.005 0.000 ARG o 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 291 time to evaluate : 6.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 264 MET cc_start: 0.7887 (tmm) cc_final: 0.7375 (ttp) REVERT: p 43 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8647 (p) REVERT: p 264 MET cc_start: 0.7981 (tmm) cc_final: 0.7422 (ttp) REVERT: s 46 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8247 (ptt-90) REVERT: t 125 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8113 (tp) REVERT: v 46 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8247 (ptt-90) REVERT: w 125 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8154 (tp) outliers start: 76 outliers final: 59 residues processed: 343 average time/residue: 0.7009 time to fit residues: 416.7138 Evaluate side-chains 345 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 281 time to evaluate : 6.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain b residue 86 VAL Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 11 LYS Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 125 VAL Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain j residue 118 LYS Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 107 MET Chi-restraints excluded: chain m residue 222 ILE Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain n residue 508 VAL Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 105 ILE Chi-restraints excluded: chain o residue 508 VAL Chi-restraints excluded: chain p residue 43 VAL Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 107 MET Chi-restraints excluded: chain p residue 222 ILE Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 239 THR Chi-restraints excluded: chain q residue 508 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 100 ASP Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 500 GLN Chi-restraints excluded: chain r residue 506 TRP Chi-restraints excluded: chain r residue 508 VAL Chi-restraints excluded: chain s residue 46 ARG Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 268 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 125 ILE Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain t residue 504 ASP Chi-restraints excluded: chain u residue 62 ASP Chi-restraints excluded: chain u residue 321 VAL Chi-restraints excluded: chain v residue 46 ARG Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 196 MET Chi-restraints excluded: chain v residue 268 VAL Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 125 ILE Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain x residue 504 ASP Chi-restraints excluded: chain A residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 846 optimal weight: 8.9990 chunk 891 optimal weight: 9.9990 chunk 813 optimal weight: 6.9990 chunk 867 optimal weight: 10.0000 chunk 522 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 681 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 784 optimal weight: 10.0000 chunk 820 optimal weight: 10.0000 chunk 864 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 76584 Z= 0.424 Angle : 0.618 9.895 104136 Z= 0.327 Chirality : 0.047 0.206 12012 Planarity : 0.005 0.062 13488 Dihedral : 5.054 25.502 10590 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.97 % Allowed : 10.19 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.08), residues: 9774 helix: 1.18 (0.11), residues: 2172 sheet: 0.38 (0.12), residues: 2004 loop : -1.82 (0.07), residues: 5598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP q 506 HIS 0.008 0.002 HIS q 429 PHE 0.017 0.002 PHE q 343 TYR 0.018 0.002 TYR o 350 ARG 0.007 0.001 ARG o 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 286 time to evaluate : 6.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 43 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8658 (p) REVERT: m 264 MET cc_start: 0.7942 (tmm) cc_final: 0.7510 (ttp) REVERT: o 43 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8850 (m) REVERT: p 43 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8658 (p) REVERT: p 107 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7977 (mtp) REVERT: p 264 MET cc_start: 0.7952 (tmm) cc_final: 0.7406 (ttp) REVERT: r 43 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8864 (m) REVERT: s 46 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8148 (ptt-90) REVERT: t 125 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8192 (tp) REVERT: v 46 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8106 (ptt-90) REVERT: w 125 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8200 (tp) REVERT: x 338 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7106 (mm110) outliers start: 78 outliers final: 61 residues processed: 347 average time/residue: 0.7192 time to fit residues: 435.1326 Evaluate side-chains 355 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 284 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain b residue 86 VAL Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain f residue 94 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 81 ILE Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 125 VAL Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain j residue 118 LYS Chi-restraints excluded: chain k residue 125 VAL Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain l residue 145 ASP Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 107 MET Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 222 ILE Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain n residue 508 VAL Chi-restraints excluded: chain o residue 43 VAL Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 105 ILE Chi-restraints excluded: chain o residue 508 VAL Chi-restraints excluded: chain p residue 43 VAL Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 107 MET Chi-restraints excluded: chain p residue 186 VAL Chi-restraints excluded: chain p residue 222 ILE Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 239 THR Chi-restraints excluded: chain q residue 508 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 100 ASP Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 107 MET Chi-restraints excluded: chain r residue 500 GLN Chi-restraints excluded: chain r residue 506 TRP Chi-restraints excluded: chain r residue 508 VAL Chi-restraints excluded: chain s residue 46 ARG Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 268 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 43 VAL Chi-restraints excluded: chain t residue 125 ILE Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain t residue 504 ASP Chi-restraints excluded: chain u residue 62 ASP Chi-restraints excluded: chain u residue 321 VAL Chi-restraints excluded: chain v residue 46 ARG Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 196 MET Chi-restraints excluded: chain v residue 268 VAL Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 125 ILE Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 338 GLN Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain x residue 504 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 569 optimal weight: 0.8980 chunk 917 optimal weight: 7.9990 chunk 559 optimal weight: 5.9990 chunk 435 optimal weight: 3.9990 chunk 637 optimal weight: 1.9990 chunk 962 optimal weight: 0.9990 chunk 885 optimal weight: 6.9990 chunk 766 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 591 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 75 GLN p 75 GLN ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 76584 Z= 0.167 Angle : 0.482 8.504 104136 Z= 0.253 Chirality : 0.043 0.197 12012 Planarity : 0.004 0.061 13488 Dihedral : 4.439 25.233 10590 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.69 % Allowed : 10.55 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.08), residues: 9774 helix: 1.50 (0.11), residues: 2190 sheet: 0.46 (0.12), residues: 1962 loop : -1.62 (0.07), residues: 5622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP q 506 HIS 0.004 0.001 HIS p 429 PHE 0.016 0.001 PHE r 343 TYR 0.010 0.001 TYR p 350 ARG 0.004 0.000 ARG g 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19548 Ramachandran restraints generated. 9774 Oldfield, 0 Emsley, 9774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 302 time to evaluate : 6.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 142 ASP cc_start: 0.9075 (m-30) cc_final: 0.8838 (m-30) REVERT: j 111 MET cc_start: 0.8743 (tpt) cc_final: 0.7846 (tpt) REVERT: p 264 MET cc_start: 0.7855 (tmm) cc_final: 0.7215 (ttp) REVERT: r 43 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8826 (m) REVERT: s 46 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8302 (ptt-90) REVERT: u 338 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.6877 (mm110) REVERT: x 338 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.6861 (mm110) outliers start: 56 outliers final: 39 residues processed: 343 average time/residue: 0.7116 time to fit residues: 422.1963 Evaluate side-chains 323 residues out of total 8112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 280 time to evaluate : 6.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain b residue 86 VAL Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain f residue 86 VAL Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 133 GLU Chi-restraints excluded: chain i residue 125 VAL Chi-restraints excluded: chain i residue 145 ASP Chi-restraints excluded: chain j residue 41 ASP Chi-restraints excluded: chain j residue 118 LYS Chi-restraints excluded: chain k residue 133 GLU Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 239 THR Chi-restraints excluded: chain n residue 508 VAL Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 508 VAL Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 239 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 100 ASP Chi-restraints excluded: chain r residue 500 GLN Chi-restraints excluded: chain r residue 506 TRP Chi-restraints excluded: chain s residue 46 ARG Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 489 ASP Chi-restraints excluded: chain t residue 489 ASP Chi-restraints excluded: chain u residue 338 GLN Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 489 ASP Chi-restraints excluded: chain w residue 489 ASP Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 338 GLN Chi-restraints excluded: chain x residue 489 ASP Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 608 optimal weight: 10.0000 chunk 816 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 706 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 767 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 788 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.067276 restraints weight = 150894.736| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.10 r_work: 0.2693 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 76584 Z= 0.217 Angle : 0.497 8.644 104136 Z= 0.260 Chirality : 0.044 0.187 12012 Planarity : 0.004 0.061 13488 Dihedral : 4.414 25.005 10590 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.66 % Allowed : 10.61 % Favored : 88.73 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.08), residues: 9774 helix: 1.57 (0.12), residues: 2184 sheet: 0.54 (0.12), residues: 1932 loop : -1.61 (0.07), residues: 5658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP q 506 HIS 0.006 0.001 HIS q 429 PHE 0.016 0.001 PHE r 343 TYR 0.012 0.001 TYR o 350 ARG 0.004 0.000 ARG g 16 =============================================================================== Job complete usr+sys time: 10231.56 seconds wall clock time: 184 minutes 47.99 seconds (11087.99 seconds total)