Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 19:52:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/07_2023/7elm_31185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/07_2023/7elm_31185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/07_2023/7elm_31185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/07_2023/7elm_31185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/07_2023/7elm_31185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/07_2023/7elm_31185.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 46 5.16 5 C 29098 2.51 5 N 8735 2.21 5 O 9402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "K GLU 220": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 224": "OE1" <-> "OE2" Residue "M GLU 321": "OE1" <-> "OE2" Residue "N GLU 38": "OE1" <-> "OE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 340": "OE1" <-> "OE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "P GLU 38": "OE1" <-> "OE2" Residue "P TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "Q GLU 169": "OE1" <-> "OE2" Residue "Q GLU 283": "OE1" <-> "OE2" Residue "R GLU 15": "OE1" <-> "OE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "R GLU 197": "OE1" <-> "OE2" Residue "S GLU 14": "OE1" <-> "OE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S GLU 124": "OE1" <-> "OE2" Residue "S GLU 125": "OE1" <-> "OE2" Residue "S PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 169": "OE1" <-> "OE2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 157": "OE1" <-> "OE2" Residue "U GLU 158": "OE1" <-> "OE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 47399 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 2015 Classifications: {'peptide': 417} Incomplete info: {'backbone_only': 298, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 392} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1377 Unresolved non-hydrogen angles: 1978 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 378 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 20, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 8, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 743 Chain: "B" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2204 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 128 Chain: "C" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2139 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2531 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2590 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 324} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2577 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2517 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2490 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "K" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2065 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 301, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 2015 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 380 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 21, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 10, 'HIS:plan': 11, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 772 Chain: "I" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2321 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2227 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2565 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "O" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2562 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2581 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2529 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1431 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 Conformer: "B" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 bond proxies already assigned to first conformer: 1462 Chain: "U" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "V" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "J" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 15, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 35} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 24, 'rna3p': 35} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 22.70, per 1000 atoms: 0.48 Number of scatterers: 47399 At special positions: 0 Unit cell: (166.501, 160.056, 236.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 118 15.00 O 9402 8.00 N 8735 7.00 C 29098 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: 17.84 Conformation dependent library (CDL) restraints added in 7.3 seconds 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10324 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 93 sheets defined 33.5% alpha, 20.7% beta 12 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 12.35 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 removed outlier: 3.615A pdb=" N SER A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 51 through 60 removed outlier: 4.172A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.611A pdb=" N ILE A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.875A pdb=" N SER A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.958A pdb=" N SER A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.612A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.520A pdb=" N ARG A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.235A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.471A pdb=" N GLY A 292 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.778A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 343 removed outlier: 5.394A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.522A pdb=" N GLN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.066A pdb=" N VAL A 387 " --> pdb=" O TRP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 432 removed outlier: 3.918A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.998A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.605A pdb=" N LEU B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.995A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 121' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.559A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.971A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.832A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.592A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.766A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.512A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.593A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.517A pdb=" N LEU F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.513A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.618A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 63 through 72 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.575A pdb=" N ARG H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'K' and resid 15 through 29 removed outlier: 3.786A pdb=" N SER K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 46 removed outlier: 3.931A pdb=" N LYS K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 60 removed outlier: 4.138A pdb=" N ASP K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 124 removed outlier: 4.086A pdb=" N SER K 122 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN K 124 " --> pdb=" O PHE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 134 Processing helix chain 'K' and resid 140 through 146 removed outlier: 4.145A pdb=" N SER K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 163 removed outlier: 3.972A pdb=" N THR K 163 " --> pdb=" O PHE K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 176 removed outlier: 3.744A pdb=" N ALA K 175 " --> pdb=" O HIS K 172 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS K 176 " --> pdb=" O SER K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 176' Processing helix chain 'K' and resid 195 through 211 Processing helix chain 'K' and resid 212 through 224 Processing helix chain 'K' and resid 282 through 287 removed outlier: 3.934A pdb=" N PHE K 287 " --> pdb=" O HIS K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 292 removed outlier: 4.423A pdb=" N GLY K 292 " --> pdb=" O HIS K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 307 removed outlier: 3.558A pdb=" N LEU K 307 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 342 removed outlier: 4.680A pdb=" N ARG K 320 " --> pdb=" O PHE K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 363 Processing helix chain 'K' and resid 372 through 376 Processing helix chain 'K' and resid 383 through 399 removed outlier: 3.841A pdb=" N VAL K 387 " --> pdb=" O TRP K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 407 Processing helix chain 'K' and resid 408 through 432 removed outlier: 4.022A pdb=" N ALA K 412 " --> pdb=" O SER K 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.591A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 removed outlier: 3.784A pdb=" N ALA I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 removed outlier: 4.037A pdb=" N LEU I 112 " --> pdb=" O ASN I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 131 Processing helix chain 'I' and resid 132 through 136 removed outlier: 3.801A pdb=" N VAL I 135 " --> pdb=" O PRO I 132 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA I 136 " --> pdb=" O ASP I 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 132 through 136' Processing helix chain 'L' and resid 33 through 48 removed outlier: 4.067A pdb=" N PHE L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.510A pdb=" N LEU L 52 " --> pdb=" O GLY L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 121 removed outlier: 4.000A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS L 121 " --> pdb=" O GLY L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 116 through 121' Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 165 through 178 Processing helix chain 'L' and resid 189 through 201 Processing helix chain 'L' and resid 207 through 214 removed outlier: 3.540A pdb=" N ASP L 211 " --> pdb=" O ALA L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.605A pdb=" N VAL L 295 " --> pdb=" O PRO L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 3.993A pdb=" N LEU L 301 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU L 302 " --> pdb=" O SER L 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 36 removed outlier: 3.550A pdb=" N SER M 36 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 129 removed outlier: 3.507A pdb=" N ARG M 115 " --> pdb=" O ASP M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 144 Processing helix chain 'M' and resid 189 through 204 Processing helix chain 'M' and resid 256 through 265 Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 319 through 333 Processing helix chain 'N' and resid 32 through 36 removed outlier: 3.780A pdb=" N SER N 36 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 73 removed outlier: 3.584A pdb=" N SER N 73 " --> pdb=" O ALA N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 129 Processing helix chain 'N' and resid 131 through 144 Processing helix chain 'N' and resid 189 through 204 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 303 through 313 Processing helix chain 'N' and resid 319 through 333 Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.913A pdb=" N SER O 36 " --> pdb=" O ARG O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.598A pdb=" N ARG O 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 removed outlier: 3.567A pdb=" N SER O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 129 Processing helix chain 'O' and resid 131 through 144 Processing helix chain 'O' and resid 189 through 204 Processing helix chain 'O' and resid 256 through 265 Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 319 through 333 Processing helix chain 'P' and resid 32 through 36 removed outlier: 3.677A pdb=" N SER P 36 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 72 removed outlier: 3.847A pdb=" N LEU P 67 " --> pdb=" O ASP P 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP P 68 " --> pdb=" O PRO P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 129 Processing helix chain 'P' and resid 131 through 144 Processing helix chain 'P' and resid 189 through 204 Processing helix chain 'P' and resid 256 through 265 Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 319 through 333 Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.594A pdb=" N SER Q 36 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.765A pdb=" N SER Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 129 Processing helix chain 'Q' and resid 131 through 144 Processing helix chain 'Q' and resid 189 through 204 Processing helix chain 'Q' and resid 256 through 265 Processing helix chain 'Q' and resid 303 through 313 Processing helix chain 'Q' and resid 319 through 333 Processing helix chain 'R' and resid 32 through 36 removed outlier: 3.511A pdb=" N SER R 36 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 62 removed outlier: 4.002A pdb=" N ARG R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 72 Processing helix chain 'R' and resid 111 through 129 Processing helix chain 'R' and resid 131 through 144 Processing helix chain 'R' and resid 189 through 204 Processing helix chain 'R' and resid 256 through 265 Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'R' and resid 319 through 333 Processing helix chain 'S' and resid 16 through 36 Processing helix chain 'S' and resid 63 through 72 removed outlier: 3.952A pdb=" N ALA S 72 " --> pdb=" O ARG S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 3.990A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS S 120 " --> pdb=" O LEU S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 131 Processing helix chain 'S' and resid 132 through 136 removed outlier: 3.772A pdb=" N VAL S 135 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA S 136 " --> pdb=" O ASP S 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 132 through 136' Processing helix chain 'U' and resid 47 through 70 removed outlier: 3.682A pdb=" N PHE U 55 " --> pdb=" O VAL U 51 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 136 Processing helix chain 'U' and resid 140 through 147 removed outlier: 3.549A pdb=" N ILE U 143 " --> pdb=" O LEU U 140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU U 147 " --> pdb=" O THR U 144 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 Processing helix chain 'U' and resid 180 through 188 Processing helix chain 'U' and resid 191 through 197 Processing helix chain 'U' and resid 198 through 200 No H-bonds generated for 'chain 'U' and resid 198 through 200' Processing helix chain 'U' and resid 211 through 222 Processing helix chain 'V' and resid 47 through 70 removed outlier: 3.683A pdb=" N PHE V 55 " --> pdb=" O VAL V 51 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP V 57 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 136 Processing helix chain 'V' and resid 140 through 147 removed outlier: 3.550A pdb=" N ILE V 143 " --> pdb=" O LEU V 140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU V 147 " --> pdb=" O THR V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 168 Processing helix chain 'V' and resid 180 through 188 Processing helix chain 'V' and resid 191 through 197 Processing helix chain 'V' and resid 198 through 200 No H-bonds generated for 'chain 'V' and resid 198 through 200' Processing helix chain 'V' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 removed outlier: 7.140A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 182 removed outlier: 5.227A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 280 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 removed outlier: 4.050A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG B 218 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.553A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 removed outlier: 5.038A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.502A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.830A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 49 Processing sheet with id=AB7, first strand: chain 'D' and resid 266 through 268 Processing sheet with id=AB8, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.627A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 108 through 109 Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.521A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.816A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER E 243 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.594A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 108 through 109 Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.908A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 45 through 51 removed outlier: 7.482A pdb=" N SER F 243 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR F 78 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD1, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD2, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.983A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD5, first strand: chain 'G' and resid 44 through 50 removed outlier: 7.520A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD7, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.602A pdb=" N VAL G 288 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.783A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.915A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.277A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.277A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N HIS U 26 " --> pdb=" O THR U 41 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR U 41 " --> pdb=" O HIS U 26 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP U 28 " --> pdb=" O ILE U 39 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE U 39 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU U 30 " --> pdb=" O MET U 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE5, first strand: chain 'K' and resid 178 through 181 Processing sheet with id=AE6, first strand: chain 'K' and resid 178 through 181 removed outlier: 7.276A pdb=" N PHE L 279 " --> pdb=" O ALA L 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA L 257 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU L 281 " --> pdb=" O TYR L 255 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR L 255 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU L 283 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP L 247 " --> pdb=" O TRP L 289 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA L 253 " --> pdb=" O TRP L 316 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP L 316 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU L 313 " --> pdb=" O GLU L 308 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 232 through 234 removed outlier: 3.877A pdb=" N GLU K 234 " --> pdb=" O CYS L 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS L 217 " --> pdb=" O GLU K 234 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG L 218 " --> pdb=" O ARG L 242 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 262 through 264 removed outlier: 4.146A pdb=" N PHE L 81 " --> pdb=" O ILE K 240 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AF1, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AF2, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AF3, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AF4, first strand: chain 'I' and resid 172 through 173 removed outlier: 3.907A pdb=" N GLY I 172 " --> pdb=" O LYS I 180 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.005A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.005A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA L 103 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU L 109 " --> pdb=" O PRO L 13 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU L 11 " --> pdb=" O LEU L 111 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 113 " --> pdb=" O LEU L 9 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU L 9 " --> pdb=" O VAL L 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 108 through 109 removed outlier: 3.530A pdb=" N ALA M 108 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.184A pdb=" N ALA M 157 " --> pdb=" O ARG M 218 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.890A pdb=" N ALA M 253 " --> pdb=" O MET M 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 44 through 47 Processing sheet with id=AG2, first strand: chain 'M' and resid 266 through 268 Processing sheet with id=AG3, first strand: chain 'N' and resid 108 through 109 removed outlier: 3.551A pdb=" N ALA N 108 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AG5, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AG6, first strand: chain 'N' and resid 44 through 50 Processing sheet with id=AG7, first strand: chain 'N' and resid 266 through 268 Processing sheet with id=AG8, first strand: chain 'N' and resid 287 through 288 removed outlier: 3.661A pdb=" N LYS N 293 " --> pdb=" O VAL N 288 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 108 through 109 Processing sheet with id=AH1, first strand: chain 'O' and resid 19 through 20 removed outlier: 4.721A pdb=" N LEU O 210 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL O 158 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP O 177 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL O 160 " --> pdb=" O ARG O 175 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG O 175 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE O 162 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR O 173 " --> pdb=" O ILE O 162 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS O 164 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AH3, first strand: chain 'O' and resid 44 through 50 removed outlier: 7.767A pdb=" N SER O 243 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR O 78 " --> pdb=" O SER O 243 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 287 through 288 removed outlier: 3.545A pdb=" N LYS O 293 " --> pdb=" O VAL O 288 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 108 through 109 Processing sheet with id=AH6, first strand: chain 'P' and resid 19 through 20 removed outlier: 4.700A pdb=" N LEU P 210 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL P 158 " --> pdb=" O ASP P 177 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP P 177 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL P 160 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG P 175 " --> pdb=" O VAL P 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE P 162 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR P 173 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS P 164 " --> pdb=" O ALA P 171 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 19 through 20 Processing sheet with id=AH8, first strand: chain 'P' and resid 44 through 51 removed outlier: 7.464A pdb=" N SER P 243 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR P 78 " --> pdb=" O SER P 243 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P' and resid 266 through 268 Processing sheet with id=AI1, first strand: chain 'P' and resid 287 through 288 Processing sheet with id=AI2, first strand: chain 'Q' and resid 108 through 109 Processing sheet with id=AI3, first strand: chain 'Q' and resid 19 through 20 removed outlier: 4.497A pdb=" N LEU Q 210 " --> pdb=" O ILE Q 165 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL Q 158 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP Q 177 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL Q 160 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG Q 175 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE Q 162 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR Q 173 " --> pdb=" O ILE Q 162 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS Q 164 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AI5, first strand: chain 'Q' and resid 44 through 51 removed outlier: 4.037A pdb=" N ASN Q 75 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER Q 243 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR Q 78 " --> pdb=" O SER Q 243 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 266 through 268 Processing sheet with id=AI7, first strand: chain 'Q' and resid 287 through 288 removed outlier: 3.559A pdb=" N LYS Q 293 " --> pdb=" O VAL Q 288 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 108 through 109 Processing sheet with id=AI9, first strand: chain 'R' and resid 19 through 20 removed outlier: 4.461A pdb=" N LEU R 210 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL R 158 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP R 177 " --> pdb=" O VAL R 158 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL R 160 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG R 175 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE R 162 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR R 173 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS R 164 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ2, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.256A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.256A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N HIS V 26 " --> pdb=" O THR V 41 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR V 41 " --> pdb=" O HIS V 26 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP V 28 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE V 39 " --> pdb=" O TRP V 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU V 30 " --> pdb=" O MET V 37 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 266 through 268 Processing sheet with id=AJ5, first strand: chain 'R' and resid 287 through 288 removed outlier: 3.748A pdb=" N VAL R 288 " --> pdb=" O LYS R 293 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS R 293 " --> pdb=" O VAL R 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ7, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ8, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AJ9, first strand: chain 'S' and resid 100 through 102 removed outlier: 3.590A pdb=" N PHE S 155 " --> pdb=" O LEU S 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU S 157 " --> pdb=" O VAL S 144 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'S' and resid 172 through 173 removed outlier: 3.586A pdb=" N GLY S 172 " --> pdb=" O LYS S 180 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'U' and resid 85 through 91 removed outlier: 7.747A pdb=" N VAL U 85 " --> pdb=" O ASN U 79 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN U 79 " --> pdb=" O VAL U 85 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR U 109 " --> pdb=" O VAL U 123 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'V' and resid 85 through 91 removed outlier: 7.748A pdb=" N VAL V 85 " --> pdb=" O ASN V 79 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN V 79 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR V 109 " --> pdb=" O VAL V 123 " (cutoff:3.500A) 2128 hydrogen bonds defined for protein. 5805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 21.08 Time building geometry restraints manager: 19.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9668 1.33 - 1.45: 12056 1.45 - 1.57: 26547 1.57 - 1.69: 238 1.69 - 1.81: 71 Bond restraints: 48580 Sorted by residual: bond pdb=" C ARG I 73 " pdb=" N PRO I 74 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 8.93e+00 bond pdb=" C ARG S 73 " pdb=" N PRO S 74 " ideal model delta sigma weight residual 1.334 1.357 -0.023 8.40e-03 1.42e+04 7.47e+00 bond pdb=" CB ILE R 199 " pdb=" CG2 ILE R 199 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.76e+00 bond pdb=" CG1 ILE R 199 " pdb=" CD1 ILE R 199 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.88e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.54e+00 ... (remaining 48575 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.78: 2047 106.78 - 113.78: 26238 113.78 - 120.79: 21493 120.79 - 127.80: 15946 127.80 - 134.81: 657 Bond angle restraints: 66381 Sorted by residual: angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 110.05 102.48 7.57 1.09e+00 8.42e-01 4.82e+01 angle pdb=" N LEU B 181 " pdb=" CA LEU B 181 " pdb=" C LEU B 181 " ideal model delta sigma weight residual 109.81 121.43 -11.62 2.21e+00 2.05e-01 2.76e+01 angle pdb=" C ALA V 205 " pdb=" N ASN V 206 " pdb=" CA ASN V 206 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ALA U 205 " pdb=" N ASN U 206 " pdb=" CA ASN U 206 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C PHE S 15 " pdb=" N PRO S 16 " pdb=" CA PRO S 16 " ideal model delta sigma weight residual 119.66 123.03 -3.37 7.20e-01 1.93e+00 2.19e+01 ... (remaining 66376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 27113 35.04 - 70.08: 694 70.08 - 105.12: 68 105.12 - 140.16: 2 140.16 - 175.20: 12 Dihedral angle restraints: 27889 sinusoidal: 11248 harmonic: 16641 Sorted by residual: dihedral pdb=" O4' U J 39 " pdb=" C1' U J 39 " pdb=" N1 U J 39 " pdb=" C2 U J 39 " ideal model delta sinusoidal sigma weight residual 200.00 46.69 153.31 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' C J 37 " pdb=" C1' C J 37 " pdb=" N1 C J 37 " pdb=" C2 C J 37 " ideal model delta sinusoidal sigma weight residual 200.00 47.81 152.19 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" O4' U T 33 " pdb=" C1' U T 33 " pdb=" N1 U T 33 " pdb=" C2 U T 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.98 147.02 1 1.50e+01 4.44e-03 7.85e+01 ... (remaining 27886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 6195 0.070 - 0.139: 898 0.139 - 0.209: 85 0.209 - 0.278: 16 0.278 - 0.348: 3 Chirality restraints: 7197 Sorted by residual: chirality pdb=" CB ILE S 40 " pdb=" CA ILE S 40 " pdb=" CG1 ILE S 40 " pdb=" CG2 ILE S 40 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE F 232 " pdb=" CA ILE F 232 " pdb=" CG1 ILE F 232 " pdb=" CG2 ILE F 232 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA LEU B 181 " pdb=" N LEU B 181 " pdb=" C LEU B 181 " pdb=" CB LEU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 7194 not shown) Planarity restraints: 8509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 263 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 264 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 297 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO E 298 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 263 " -0.039 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO L 264 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO L 264 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 264 " -0.032 5.00e-02 4.00e+02 ... (remaining 8506 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 214 2.45 - 3.06: 28040 3.06 - 3.68: 73331 3.68 - 4.29: 108563 4.29 - 4.90: 177122 Nonbonded interactions: 387270 Sorted by model distance: nonbonded pdb=" CD2 LEU B 181 " pdb=" CD PRO B 182 " model vdw 1.839 3.860 nonbonded pdb=" O ASN N 75 " pdb=" OD1 ASN N 75 " model vdw 2.004 3.040 nonbonded pdb=" O ASP U 53 " pdb=" OD1 ASP U 53 " model vdw 2.063 3.040 nonbonded pdb=" O2' G J 40 " pdb=" C5' G J 41 " model vdw 2.103 3.440 nonbonded pdb=" CG PRO S 16 " pdb=" O2' G T 41 " model vdw 2.180 3.440 ... (remaining 387265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 103 or (resid 104 through 167 and (name N or na \ me CA or name C or name O )) or resid 168 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 through 202 or (resid \ 203 through 205 and (name N or name CA or name C or name O or name CB )) or resi \ d 206 through 223 or (resid 224 and (name N or name CA or name C or name O or na \ me CB )) or resid 225 through 227 or (resid 228 and (name N or name CA or name C \ or name O or name CB )) or resid 229 through 434)) selection = (chain 'K' and (resid 11 through 197 or (resid 198 and (name N or name CA or nam \ e C or name O or name CB )) or resid 199 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 or (resid 207 and (name \ N or name CA or name C or name O or name CB )) or resid 208 through 209 or (res \ id 210 and (name N or name CA or name C or name O or name CB )) or resid 211 thr \ ough 218 or (resid 219 through 222 and (name N or name CA or name C or name O or \ name CB )) or resid 223 through 226 or (resid 227 through 228 and (name N or na \ me CA or name C or name O or name CB )) or resid 229 through 257 or (resid 258 t \ hrough 259 and (name N or name CA or name C or name O or name CB )) or resid 260 \ through 265 or (resid 266 through 269 and (name N or name CA or name C or name \ O )) or resid 270 or resid 278 through 434)) } ncs_group { reference = (chain 'B' and (resid 3 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 75 or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB )) or resid 78 through 149 \ or (resid 150 through 151 and (name N or name CA or name C or name O or name CB \ )) or resid 152 through 166 or (resid 167 and (name N or name CA or name C or na \ me O or name CB )) or resid 168 through 188 or (resid 189 through 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 239 or (resi \ d 240 and (name N or name CA or name C or name O or name CB )) or resid 241 thro \ ugh 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) o \ r resid 287 through 322)) selection = (chain 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 51 or (resid 52 and (name N or na \ me CA or name C or name O or name CB )) or resid 53 through 62 or (resid 63 and \ (name N or name CA or name C or name O or name CB )) or resid 64 through 66 or ( \ resid 67 through 68 and (name N or name CA or name C or name O or name CB )) or \ resid 69 through 76 or (resid 77 and (name N or name CA or name C or name O or n \ ame CB )) or resid 78 through 93 or (resid 94 through 96 and (name N or name CA \ or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (nam \ e N or name CA or name C or name O or name CB )) or resid 109 through 112 or (re \ sid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 th \ rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 through 127 or (resid 128 and (name N or name CA or name C or name \ O or name CB )) or resid 129 through 146 or (resid 147 and (name N or name CA o \ r name C or name O or name CB )) or resid 148 through 157 or (resid 158 and (nam \ e N or name CA or name C or name O or name CB )) or resid 159 through 160 or (re \ sid 161 through 162 and (name N or name CA or name C or name O or name CB )) or \ resid 163 through 168 or (resid 169 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 or (resid 172 through 173 and (name N or n \ ame CA or name C or name O or name CB )) or resid 174 or (resid 175 and (name N \ or name CA or name C or name O or name CB )) or resid 176 through 177 or (resid \ 178 and (name N or name CA or name C or name O or name CB )) or resid 179 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 197 or (resid 198 and (name N or name CA or name C or name O o \ r name CB )) or resid 199 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 213 or (resid 214 and (name N \ or name CA or name C or name O or name CB )) or resid 215 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 223 or (resid 239 through 240 and (name N or name CA or name C or name O or na \ me CB )) or resid 241 through 265 or (resid 266 and (name N or name CA or name C \ or name O or name CB )) or resid 267 through 276 or (resid 277 and (name N or n \ ame CA or name C or name O or name CB )) or resid 278 through 281 or (resid 282 \ and (name N or name CA or name C or name O or name CB )) or resid 283 through 28 \ 9 or (resid 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 300 or (resid 301 and (name N or name CA or name C or name O or na \ me CB )) or resid 302 through 304 or (resid 305 and (name N or name CA or name C \ or name O or name CB )) or resid 306 through 313 or (resid 314 and (name N or n \ ame CA or name C or name O or name CB )) or resid 315 through 319 or (resid 320 \ and (name N or name CA or name C or name O or name CB )) or resid 321 through 32 \ 2)) } ncs_group { reference = (chain 'C' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 48 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 79 or (re \ sid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or \ resid 99 through 108 or (resid 109 through 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 through 113 or (resid 114 through 115 and ( \ name N or name CA or name C or name O or name CB )) or resid 116 or (resid 117 t \ hrough 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ through 132 or (resid 133 and (name N or name CA or name C or name O or name CB \ )) or resid 134 through 149 or (resid 150 and (name N or name CA or name C or n \ ame O or name CB )) or resid 151 through 161 or (resid 162 and (name N or name C \ A or name C or name O or name CB )) or resid 163 or (resid 164 and (name N or na \ me CA or name C or name O or name CB )) or resid 165 through 207 or (resid 208 a \ nd (name N or name CA or name C or name O or name CB )) or resid 209 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 273 or (resid 274 through 275 and (name N or name C \ A or name C or name O or name CB )) or resid 276 or (resid 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 through 282 or (resid 283 a \ nd (name N or name CA or name C or name O or name CB )) or resid 284 or (resid 2 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 286 through \ 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) or r \ esid 308 through 320 or (resid 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 326 or (resid 327 through 328 and (name N or na \ me CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name N o \ r name CA or name C or name O or 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(name N or name CA or name C or name O or name CB )) \ or resid 272 through 273 or (resid 274 through 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or \ name C or name O or name CB )) or resid 278 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 or (resid 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 290 or \ (resid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 \ through 295 or (resid 296 through 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 301 or (resid 302 through 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 through 306 or (res \ id 307 and (name N or name CA or name C or name O or name CB )) or resid 308 thr \ ough 313 or (resid 314 and (name N or name CA or name C or name O or name CB )) \ or resid 315 through 320 or (resid 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 323 or (resid 324 and (name N or name CA or \ name C or name O or name CB )) or resid 325 through 326 or (resid 327 through 3 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 329 or (res \ id 330 and (name N or name CA or name C or name O or name CB )) or resid 331 thr \ ough 338)) selection = (chain 'N' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or nam \ e CA or name C or name O or name CB )) or resid 286 through 290 or (resid 291 an \ d (name N or name CA or name C or name O or name CB )) or resid 292 through 295 \ or (resid 296 through 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 313 or ( \ resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 320 or (resid 321 and (name N or name CA or name C or name O or name CB \ )) or resid 322 through 323 or (resid 324 and (name N or name CA or name C or na \ me O or name CB )) or resid 325 through 326 or (resid 327 through 328 and (name \ N or name CA or name C or name O or name CB )) or resid 329 or (resid 330 and (n \ ame N or name CA or name C or name O or name CB )) or resid 331 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or nam \ e CA or name C or name O or name CB )) or resid 286 through 290 or (resid 291 an \ d (name N or name CA or name C or name O or name CB )) or resid 292 through 295 \ or (resid 296 through 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 313 or ( \ resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 320 or (resid 321 and (name N or name CA or name C or name O or name CB \ )) or resid 322 through 323 or (resid 324 and (name N or name CA or name C or na \ me O or name CB )) or resid 325 through 326 or (resid 327 through 328 and (name \ N or name CA or name C or name O or name CB )) or resid 329 or (resid 330 and (n \ ame N or name CA or name C or name O or name CB )) or resid 331 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 284 or (resid 285 and (name N or name CA \ or name C or name O or name CB )) or resid 286 through 290 or (resid 291 and (n \ ame N or name CA or name C or name O or name CB )) or resid 292 through 295 or ( \ resid 296 through 297 and (name N or name CA or name C or name O or name CB )) o \ r resid 298 or (resid 299 and (name N or name CA or name C or name O or name CB \ )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA or \ name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (name \ N or name CA or name C or name O or name CB )) or resid 308 through 313 or (resi \ d 314 and (name N or name CA or name C or name O or name CB )) or resid 315 thro \ ugh 320 or (resid 321 and (name N or name CA or name C or name O or name CB )) o \ r resid 322 through 323 or (resid 324 and (name N or name CA or name C or name O \ or name CB )) or resid 325 through 326 or (resid 327 through 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name \ N or name CA or name C or name O or name CB )) or resid 331 through 337 or (resi \ d 338 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or nam \ e CA or name C or name O or name CB )) or resid 286 through 290 or (resid 291 an \ d (name N or name CA or name C or name O or name CB )) or resid 292 through 295 \ or (resid 296 through 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 313 or ( \ resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 323 or (resid 324 and (name N or name CA or name C or name O or name CB \ )) or resid 325 through 326 or (resid 327 through 328 and (name N or name CA or \ name C or name O or name CB )) or resid 329 or (resid 330 and (name N or name CA \ or name C or name O or name CB )) or resid 331 through 337 or (resid 338 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 113 or (r \ esid 114 through 115 and (name N or name CA or name C or name O or name CB )) or \ resid 116 or (resid 117 through 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 through 130 or (resid 131 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 1 \ 39 or (resid 140 and (name N or name CA or name C or name O or name CB )) or res \ id 141 through 149 or (resid 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 155 or (resid 156 through 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 or (resid 159 and (name N or \ name CA or name C or name O or name CB )) or resid 160 or (resid 161 through 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throu \ gh 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or \ resid 170 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 207 or (resid 208 and (name N or name CA or n \ ame C or name O or name CB )) or resid 209 or (resid 210 and (name N or name CA \ or name C or name O or name CB )) or resid 211 through 217 or (resid 218 and (na \ me N or name CA or name C or name O or name CB )) or resid 219 through 228 or (r \ esid 229 and (name N or name CA or name C or name O or name CB )) or resid 230 o \ r resid 244 through 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 249 or (resid 250 and (name N or name CA or \ name C or name O or name CB )) or resid 251 through 270 or (resid 271 and (name \ N or name CA or name C or name O or name CB )) or resid 272 through 276 or (resi \ d 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 282 or (resid 283 and (name N or name CA or name C or name O or name CB )) o \ r resid 284 or (resid 285 and (name N or name CA or name C or name O or name CB \ )) or resid 286 through 290 or (resid 291 and (name N or name CA or name C or na \ me O or name CB )) or resid 292 through 295 or (resid 296 through 297 and (name \ N or name CA or name C or name O or name CB )) or resid 298 or (resid 299 and (n \ ame N or name CA or name C or name O or name CB )) or resid 300 through 301 or ( \ resid 302 through 303 and (name N or name CA or name C or name O or name CB )) o \ r resid 304 through 306 or (resid 307 and (name N or name CA or name C or name O \ or name CB )) or resid 308 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 320 or (resid 321 and (name \ N or name CA or name C or name O or name CB )) or resid 322 through 323 or (resi \ d 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thro \ ugh 329 or (resid 330 and (name N or name CA or name C or name O or name CB )) o \ r resid 331 through 337 or (resid 338 and (name N or name CA or name C or name O \ or name CB )))) } ncs_group { reference = (chain 'I' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 142 or (resid 143 and (name N or na \ me CA or name C or name O or name CB )) or resid 144 through 152 or (resid 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 174 \ or resid 176 through 177 or (resid 178 and (name N or name CA or name C or name \ O or name CB )) or resid 179 through 187)) selection = (chain 'S' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 1.730 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: 0.040 Extract box with map and model: 11.520 Check model and map are aligned: 0.700 Set scattering table: 0.350 Process input model: 124.050 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.280 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 48580 Z= 0.360 Angle : 0.783 12.819 66381 Z= 0.451 Chirality : 0.051 0.348 7197 Planarity : 0.006 0.064 8509 Dihedral : 15.824 175.197 17565 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.91 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -3.08 (0.09), residues: 6146 helix: -2.32 (0.08), residues: 1913 sheet: 0.21 (0.15), residues: 1032 loop : -2.72 (0.09), residues: 3201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 475 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 490 average time/residue: 1.7499 time to fit residues: 1045.1913 Evaluate side-chains 277 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 5.314 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.8768 time to fit residues: 11.8082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 0.3980 chunk 471 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 161 optimal weight: 0.0980 chunk 318 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 487 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 296 optimal weight: 50.0000 chunk 362 optimal weight: 0.7980 chunk 564 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS B 129 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 240 GLN C 77 GLN C 151 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 208 HIS D 329 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN E 223 GLN E 262 ASN E 300 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN H 127 ASN H 129 GLN H 223 GLN I 108 ASN L 133 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN M 120 GLN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 GLN N 127 ASN O 144 ASN O 223 GLN ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 GLN Q 241 GLN Q 291 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 GLN S 82 HIS S 84 GLN U 2 ASN V 2 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 0.039 48580 Z= 0.169 Angle : 0.557 18.368 66381 Z= 0.295 Chirality : 0.041 0.313 7197 Planarity : 0.004 0.104 8509 Dihedral : 12.003 179.191 8134 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 6146 helix: -0.19 (0.11), residues: 1931 sheet: 0.51 (0.15), residues: 1042 loop : -2.25 (0.10), residues: 3173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 288 time to evaluate : 4.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 26 residues processed: 350 average time/residue: 1.5385 time to fit residues: 677.2446 Evaluate side-chains 271 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 5.493 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.5747 time to fit residues: 12.3883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 470 optimal weight: 4.9990 chunk 384 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 565 optimal weight: 30.0000 chunk 611 optimal weight: 5.9990 chunk 503 optimal weight: 6.9990 chunk 561 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 453 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 196 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN H 300 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** N 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 HIS ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN Q 329 ASN ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS U 154 HIS U 206 ASN V 2 ASN V 154 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.125 48580 Z= 0.528 Angle : 0.706 14.526 66381 Z= 0.371 Chirality : 0.047 0.253 7197 Planarity : 0.006 0.085 8509 Dihedral : 12.184 177.214 8134 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 6146 helix: 0.55 (0.11), residues: 1932 sheet: 0.38 (0.15), residues: 1058 loop : -2.04 (0.10), residues: 3156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 266 time to evaluate : 5.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 55 residues processed: 369 average time/residue: 1.5432 time to fit residues: 717.9047 Evaluate side-chains 282 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 5.077 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 41 residues processed: 14 average time/residue: 0.9239 time to fit residues: 24.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 8.9990 chunk 425 optimal weight: 0.9980 chunk 293 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 270 optimal weight: 0.0050 chunk 379 optimal weight: 6.9990 chunk 567 optimal weight: 0.9990 chunk 601 optimal weight: 2.9990 chunk 296 optimal weight: 50.0000 chunk 538 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 194 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 HIS O 120 GLN O 329 ASN ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN U 206 ASN V 2 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 48580 Z= 0.158 Angle : 0.534 13.368 66381 Z= 0.280 Chirality : 0.040 0.214 7197 Planarity : 0.004 0.068 8509 Dihedral : 11.864 178.838 8134 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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 (0.10), residues: 6146 helix: 1.19 (0.12), residues: 1920 sheet: 0.58 (0.15), residues: 1078 loop : -1.84 (0.10), residues: 3148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 259 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 55 residues processed: 354 average time/residue: 1.5672 time to fit residues: 703.3072 Evaluate side-chains 294 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 239 time to evaluate : 5.189 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 49 residues processed: 6 average time/residue: 0.5827 time to fit residues: 12.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 10.0000 chunk 341 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 447 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 513 optimal weight: 3.9990 chunk 415 optimal weight: 2.9990 chunk 0 optimal weight: 70.0000 chunk 307 optimal weight: 0.3980 chunk 539 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 HIS I 120 HIS ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 48580 Z= 0.260 Angle : 0.557 11.505 66381 Z= 0.291 Chirality : 0.041 0.187 7197 Planarity : 0.004 0.063 8509 Dihedral : 11.818 177.503 8134 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.38 (0.11), residues: 6146 helix: 1.43 (0.12), residues: 1914 sheet: 0.61 (0.15), residues: 1084 loop : -1.73 (0.11), residues: 3148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 245 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 71 residues processed: 346 average time/residue: 1.5459 time to fit residues: 680.6568 Evaluate side-chains 291 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 220 time to evaluate : 5.216 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 62 residues processed: 9 average time/residue: 0.7808 time to fit residues: 17.3919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 0.0970 chunk 541 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 601 optimal weight: 0.8980 chunk 499 optimal weight: 0.8980 chunk 278 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 199 optimal weight: 7.9990 chunk 315 optimal weight: 6.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS B 82 ASN B 194 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN V 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 48580 Z= 0.282 Angle : 0.568 11.326 66381 Z= 0.297 Chirality : 0.042 0.191 7197 Planarity : 0.004 0.056 8509 Dihedral : 11.826 176.727 8134 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.29 (0.11), residues: 6146 helix: 1.51 (0.12), residues: 1913 sheet: 0.68 (0.15), residues: 1081 loop : -1.68 (0.11), residues: 3152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 234 time to evaluate : 5.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 79 residues processed: 338 average time/residue: 1.5539 time to fit residues: 664.3955 Evaluate side-chains 299 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 220 time to evaluate : 5.156 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 68 residues processed: 11 average time/residue: 0.7722 time to fit residues: 19.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 0.0970 chunk 67 optimal weight: 30.0000 chunk 342 optimal weight: 5.9990 chunk 439 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 506 optimal weight: 3.9990 chunk 336 optimal weight: 0.5980 chunk 599 optimal weight: 0.9990 chunk 375 optimal weight: 4.9990 chunk 365 optimal weight: 2.9990 chunk 276 optimal weight: 50.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN R 120 GLN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 48580 Z= 0.190 Angle : 0.529 11.167 66381 Z= 0.276 Chirality : 0.040 0.180 7197 Planarity : 0.004 0.054 8509 Dihedral : 11.724 177.443 8134 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.14 (0.11), residues: 6146 helix: 1.64 (0.12), residues: 1914 sheet: 0.77 (0.15), residues: 1095 loop : -1.62 (0.11), residues: 3137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 249 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 74 residues processed: 344 average time/residue: 1.5249 time to fit residues: 670.4553 Evaluate side-chains 299 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 225 time to evaluate : 5.478 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 66 residues processed: 8 average time/residue: 0.5813 time to fit residues: 14.7968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 116 optimal weight: 0.0970 chunk 381 optimal weight: 7.9990 chunk 408 optimal weight: 0.7980 chunk 296 optimal weight: 60.0000 chunk 55 optimal weight: 8.9990 chunk 471 optimal weight: 0.8980 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN M 140 HIS M 208 HIS ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 48580 Z= 0.181 Angle : 0.528 11.181 66381 Z= 0.276 Chirality : 0.040 0.202 7197 Planarity : 0.004 0.054 8509 Dihedral : 11.633 178.014 8134 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.02 (0.11), residues: 6146 helix: 1.76 (0.12), residues: 1915 sheet: 0.83 (0.15), residues: 1095 loop : -1.55 (0.11), residues: 3136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 244 time to evaluate : 5.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 73 residues processed: 329 average time/residue: 1.5057 time to fit residues: 632.9675 Evaluate side-chains 303 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 230 time to evaluate : 5.122 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 66 residues processed: 8 average time/residue: 0.8813 time to fit residues: 17.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 7.9990 chunk 574 optimal weight: 3.9990 chunk 524 optimal weight: 2.9990 chunk 558 optimal weight: 0.6980 chunk 336 optimal weight: 1.9990 chunk 243 optimal weight: 0.1980 chunk 438 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 504 optimal weight: 0.0060 chunk 528 optimal weight: 2.9990 chunk 556 optimal weight: 30.0000 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 HIS ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN R 120 GLN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN V 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 48580 Z= 0.182 Angle : 0.532 11.091 66381 Z= 0.277 Chirality : 0.040 0.207 7197 Planarity : 0.004 0.058 8509 Dihedral : 11.608 178.668 8134 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.03 (0.11), residues: 6146 helix: 1.81 (0.12), residues: 1910 sheet: 0.86 (0.15), residues: 1092 loop : -1.52 (0.11), residues: 3144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 238 time to evaluate : 5.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 78 residues processed: 317 average time/residue: 1.5609 time to fit residues: 633.6433 Evaluate side-chains 299 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 221 time to evaluate : 5.097 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 72 residues processed: 7 average time/residue: 0.8405 time to fit residues: 15.5316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 6.9990 chunk 590 optimal weight: 0.6980 chunk 360 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 410 optimal weight: 0.7980 chunk 619 optimal weight: 7.9990 chunk 570 optimal weight: 0.9980 chunk 493 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 381 optimal weight: 8.9990 chunk 302 optimal weight: 30.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN H 127 ASN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 48580 Z= 0.205 Angle : 0.541 11.038 66381 Z= 0.283 Chirality : 0.040 0.270 7197 Planarity : 0.004 0.061 8509 Dihedral : 11.607 179.358 8134 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6146 helix: 1.83 (0.12), residues: 1903 sheet: 0.82 (0.15), residues: 1099 loop : -1.50 (0.11), residues: 3144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 235 time to evaluate : 5.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 72 residues processed: 311 average time/residue: 1.5805 time to fit residues: 628.6419 Evaluate side-chains 290 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 218 time to evaluate : 5.043 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 67 residues processed: 5 average time/residue: 0.8961 time to fit residues: 13.2250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 0.9980 chunk 525 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 454 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 494 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 507 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN G 72 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 HIS ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.140374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094420 restraints weight = 98218.888| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.96 r_work: 0.3071 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 48580 Z= 0.184 Angle : 0.543 11.226 66381 Z= 0.282 Chirality : 0.040 0.257 7197 Planarity : 0.003 0.058 8509 Dihedral : 11.580 179.468 8134 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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 (0.11), residues: 6146 helix: 1.85 (0.12), residues: 1905 sheet: 0.94 (0.15), residues: 1081 loop : -1.49 (0.11), residues: 3160 =============================================================================== Job complete usr+sys time: 13027.97 seconds wall clock time: 234 minutes 6.76 seconds (14046.76 seconds total)