Starting phenix.real_space_refine on Mon Mar 25 13:55:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eln_31186/03_2024/7eln_31186.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eln_31186/03_2024/7eln_31186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eln_31186/03_2024/7eln_31186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eln_31186/03_2024/7eln_31186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eln_31186/03_2024/7eln_31186.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eln_31186/03_2024/7eln_31186.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 170 5.49 5 S 46 5.16 5 C 29935 2.51 5 N 9012 2.21 5 O 9743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 100": "OE1" <-> "OE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 128": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 274": "OE1" <-> "OE2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "M GLU 15": "OE1" <-> "OE2" Residue "M GLU 224": "OE1" <-> "OE2" Residue "N GLU 38": "OE1" <-> "OE2" Residue "N GLU 156": "OE1" <-> "OE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 340": "OE1" <-> "OE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O GLU 197": "OE1" <-> "OE2" Residue "P GLU 38": "OE1" <-> "OE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "Q GLU 169": "OE1" <-> "OE2" Residue "R GLU 15": "OE1" <-> "OE2" Residue "R PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 156": "OE1" <-> "OE2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S GLU 125": "OE1" <-> "OE2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 96": "OE1" <-> "OE2" Residue "U GLU 157": "OE1" <-> "OE2" Residue "U GLU 158": "OE1" <-> "OE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 158": "OE1" <-> "OE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "X ARG 207": "NH1" <-> "NH2" Residue "X GLU 208": "OE1" <-> "OE2" Residue "X GLU 257": "OE1" <-> "OE2" Residue "X GLU 261": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48906 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2198 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 179 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': 11} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2144 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 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: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2587 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 324} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 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: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2523 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2487 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 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: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2571 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 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: 1445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1442 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1442 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1477 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': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 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': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "K" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "W" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "X" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "Y" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "Z" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 22.67, per 1000 atoms: 0.46 Number of scatterers: 48906 At special positions: 0 Unit cell: (167.575, 164.353, 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 170 15.00 O 9743 8.00 N 9012 7.00 C 29935 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: 17.76 Conformation dependent library (CDL) restraints added in 8.9 seconds 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10474 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 95 sheets defined 34.4% alpha, 20.7% beta 30 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 14.92 Creating SS restraints... Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.933A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.665A pdb=" N LEU B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.838A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.083A 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: 3.715A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.793A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.049A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.828A 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: 3.622A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.757A 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: 3.545A 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: 3.554A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 removed outlier: 3.549A pdb=" N LEU F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) 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: 3.758A 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: 3.560A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.606A 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: 3.522A 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 'I' and resid 16 through 36 removed outlier: 3.679A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 removed outlier: 3.684A pdb=" N LEU I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 removed outlier: 3.977A 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 'L' and resid 33 through 48 removed outlier: 4.120A pdb=" N PHE L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 116 through 121 removed outlier: 3.853A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 3.952A 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 215 removed outlier: 3.543A pdb=" N ASP L 211 " --> pdb=" O ALA L 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP L 215 " --> pdb=" O ASP L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.737A pdb=" N VAL L 295 " --> pdb=" O PRO L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.063A pdb=" N LEU L 301 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU L 302 " --> pdb=" O SER L 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 36 removed outlier: 3.768A pdb=" N SER M 36 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 129 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: 3.649A pdb=" N SER N 36 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 73 removed outlier: 3.711A 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 58 through 62 removed outlier: 3.588A pdb=" N ARG O 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 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: 3.704A pdb=" N SER P 36 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 72 removed outlier: 3.870A pdb=" N LEU P 67 " --> pdb=" O ASP P 63 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.660A pdb=" N SER Q 36 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.658A 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: 3.556A pdb=" N SER R 36 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 62 removed outlier: 4.111A 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: 3.666A pdb=" N LEU S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA S 72 " --> pdb=" O ARG S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 4.061A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.543A pdb=" N VAL S 135 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 3.879A 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: 3.673A pdb=" N PHE U 55 " --> pdb=" O VAL U 51 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 5.351A 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: 3.542A pdb=" N ILE U 143 " --> pdb=" O LEU U 140 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.673A pdb=" N PHE V 55 " --> pdb=" O VAL V 51 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP V 57 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 5.352A 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: 3.542A pdb=" N ILE V 143 " --> pdb=" O LEU V 140 " (cutoff:3.500A) removed outlier: 3.554A 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 189 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 helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 36 through 61 removed outlier: 7.071A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.543A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.662A pdb=" N ALA A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.564A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.806A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.941A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.607A pdb=" N GLY A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 433 removed outlier: 3.534A pdb=" N GLN A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 31 removed outlier: 3.532A pdb=" N GLY X 27 " --> pdb=" O GLU X 23 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS X 28 " --> pdb=" O ARG X 24 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS X 31 " --> pdb=" O GLY X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 61 removed outlier: 7.071A pdb=" N LEU X 53 " --> pdb=" O ARG X 49 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA X 54 " --> pdb=" O GLU X 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 126 removed outlier: 3.541A pdb=" N VAL X 117 " --> pdb=" O ALA X 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN X 126 " --> pdb=" O SER X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 134 Processing helix chain 'X' and resid 138 through 146 removed outlier: 3.661A pdb=" N ALA X 144 " --> pdb=" O GLU X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 164 Processing helix chain 'X' and resid 196 through 211 Processing helix chain 'X' and resid 212 through 225 Processing helix chain 'X' and resid 247 through 251 removed outlier: 3.805A pdb=" N ASN X 250 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE X 251 " --> pdb=" O PRO X 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 247 through 251' Processing helix chain 'X' and resid 253 through 258 Processing helix chain 'X' and resid 282 through 290 Processing helix chain 'X' and resid 294 through 307 removed outlier: 3.942A pdb=" N LEU X 307 " --> pdb=" O THR X 303 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 344 Processing helix chain 'X' and resid 355 through 361 Processing helix chain 'X' and resid 372 through 382 Processing helix chain 'X' and resid 384 through 399 removed outlier: 3.607A pdb=" N GLY X 388 " --> pdb=" O PRO X 384 " (cutoff:3.500A) Processing helix chain 'X' and resid 402 through 407 Processing helix chain 'X' and resid 409 through 433 removed outlier: 3.534A pdb=" N GLN X 413 " --> pdb=" O PRO X 409 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU X 432 " --> pdb=" O ILE X 428 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG X 433 " --> pdb=" O LEU X 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.941A pdb=" N GLY B 112 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY B 58 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 57 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS B 305 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.941A pdb=" N GLY B 112 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY B 58 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 57 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS B 305 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 278 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.697A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 240 through 242 removed outlier: 4.419A pdb=" N ARG B 218 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 removed outlier: 5.051A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB2, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.868A pdb=" N LYS C 293 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 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: 4.817A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 49 Processing sheet with id=AB7, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.541A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 109 Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.493A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.875A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER E 243 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.522A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 109 Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.863A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) 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 45 through 51 removed outlier: 7.537A pdb=" N SER F 243 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 78 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC9, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD1, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.631A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.942A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 50 Processing sheet with id=AD5, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD6, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.509A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.786A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 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 45 through 51 removed outlier: 4.177A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.177A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS U 26 " --> pdb=" O THR U 41 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR U 41 " --> pdb=" O HIS U 26 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP U 28 " --> pdb=" O ILE U 39 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE U 39 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU U 30 " --> pdb=" O MET U 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE4, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AE5, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AE6, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AE7, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AE8, first strand: chain 'I' and resid 172 through 173 removed outlier: 3.760A pdb=" N GLY I 172 " --> pdb=" O LYS I 180 " (cutoff:3.500A) Processing sheet with id=AE9, 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: 3.996A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing sheet with id=AF1, 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: 3.996A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA L 103 " --> pdb=" O GLN L 18 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLN L 18 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU L 105 " --> pdb=" O SER L 16 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER L 16 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL L 107 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG L 14 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 70 through 71 Processing sheet with id=AF3, first strand: chain 'L' and resid 185 through 188 removed outlier: 7.146A pdb=" N PHE L 279 " --> pdb=" O ALA L 257 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA L 257 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU L 281 " --> pdb=" O TYR L 255 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR L 255 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU L 283 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP L 247 " --> pdb=" O TRP L 289 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA L 253 " --> pdb=" O TRP L 316 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP L 316 " --> pdb=" O ALA L 253 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 185 through 188 removed outlier: 6.720A pdb=" N ARG L 278 " --> pdb=" O ALA X 191 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 240 through 242 removed outlier: 4.408A pdb=" N ARG L 218 " --> pdb=" O ARG L 242 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE X 232 " --> pdb=" O ILE L 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 108 through 109 Processing sheet with id=AF7, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.054A pdb=" N ALA M 157 " --> pdb=" O ARG M 218 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.894A pdb=" N ALA M 253 " --> pdb=" O MET M 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 44 through 47 Processing sheet with id=AG1, first strand: chain 'M' and resid 266 through 268 Processing sheet with id=AG2, first strand: chain 'N' and resid 108 through 109 removed outlier: 3.556A pdb=" N ALA N 108 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 19 through 20 removed outlier: 4.743A pdb=" N LEU N 210 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL N 158 " --> pdb=" O ASP N 177 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP N 177 " --> pdb=" O VAL N 158 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL N 160 " --> pdb=" O ARG N 175 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG N 175 " --> pdb=" O VAL N 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE N 162 " --> pdb=" O THR N 173 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR N 173 " --> pdb=" O ILE N 162 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS N 164 " --> pdb=" O ALA N 171 " (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 45 through 50 Processing sheet with id=AG6, 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=AG7, first strand: chain 'O' and resid 108 through 109 Processing sheet with id=AG8, first strand: chain 'O' and resid 19 through 20 removed outlier: 4.740A pdb=" N LEU O 210 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL O 158 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP O 177 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL O 160 " --> pdb=" O ARG O 175 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG O 175 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE O 162 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR O 173 " --> pdb=" O ILE O 162 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS O 164 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AH1, first strand: chain 'O' and resid 45 through 50 removed outlier: 7.658A pdb=" N SER O 243 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR O 78 " --> pdb=" O SER O 243 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 287 through 288 removed outlier: 3.504A pdb=" N LYS O 293 " --> pdb=" O VAL O 288 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 108 through 109 removed outlier: 3.506A pdb=" N ALA P 108 " --> pdb=" O ALA P 13 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 19 through 20 removed outlier: 4.751A pdb=" N LEU P 210 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL P 158 " --> pdb=" O ASP P 177 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP P 177 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL P 160 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG P 175 " --> pdb=" O VAL P 160 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE P 162 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR P 173 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS P 164 " --> pdb=" O ALA P 171 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 19 through 20 Processing sheet with id=AH6, first strand: chain 'P' and resid 45 through 51 removed outlier: 7.477A pdb=" N SER P 243 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR P 78 " --> pdb=" O SER P 243 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 287 through 288 Processing sheet with id=AH8, first strand: chain 'Q' and resid 108 through 109 removed outlier: 3.519A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 20 removed outlier: 4.574A pdb=" N LEU Q 210 " --> pdb=" O ILE Q 165 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA Q 157 " --> pdb=" O ARG Q 218 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL Q 158 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 4.799A 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: 4.292A pdb=" N ARG Q 175 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE Q 162 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR Q 173 " --> pdb=" O ILE Q 162 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS Q 164 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AI2, first strand: chain 'Q' and resid 45 through 51 removed outlier: 4.046A pdb=" N ASN Q 75 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 287 through 288 Processing sheet with id=AI4, first strand: chain 'R' and resid 108 through 109 Processing sheet with id=AI5, first strand: chain 'R' and resid 19 through 20 removed outlier: 4.425A pdb=" N LEU R 210 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL R 158 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP R 177 " --> pdb=" O VAL R 158 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL R 160 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG R 175 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE R 162 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR R 173 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS R 164 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AI7, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.345A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.345A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS V 26 " --> pdb=" O THR V 41 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR V 41 " --> pdb=" O HIS V 26 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP V 28 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE V 39 " --> pdb=" O TRP V 28 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU V 30 " --> pdb=" O MET V 37 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 266 through 268 Processing sheet with id=AJ1, first strand: chain 'R' and resid 287 through 288 removed outlier: 3.751A pdb=" N VAL R 288 " --> pdb=" O LYS R 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS R 293 " --> pdb=" O VAL R 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ3, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ4, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AJ5, first strand: chain 'S' and resid 100 through 102 Processing sheet with id=AJ6, first strand: chain 'S' and resid 172 through 173 removed outlier: 3.514A pdb=" N GLY S 172 " --> pdb=" O LYS S 180 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.514A pdb=" N LEU U 77 " --> pdb=" O LEU U 86 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG U 88 " --> pdb=" O LEU U 75 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU U 75 " --> pdb=" O ARG U 88 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA U 90 " --> pdb=" O ASP U 73 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP U 73 " --> pdb=" O ALA U 90 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'V' and resid 85 through 91 removed outlier: 6.515A pdb=" N LEU V 77 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG V 88 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU V 75 " --> pdb=" O ARG V 88 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA V 90 " --> pdb=" O ASP V 73 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP V 73 " --> pdb=" O ALA V 90 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AK1, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AK2, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AK3, first strand: chain 'X' and resid 65 through 66 Processing sheet with id=AK4, first strand: chain 'X' and resid 68 through 69 Processing sheet with id=AK5, first strand: chain 'X' and resid 239 through 242 2195 hydrogen bonds defined for protein. 5991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 20.67 Time building geometry restraints manager: 19.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9736 1.32 - 1.45: 12927 1.45 - 1.57: 27171 1.57 - 1.69: 338 1.69 - 1.81: 71 Bond restraints: 50243 Sorted by residual: bond pdb=" CA ASN B 149 " pdb=" C ASN B 149 " ideal model delta sigma weight residual 1.523 1.576 -0.053 1.34e-02 5.57e+03 1.57e+01 bond pdb=" C ARG V 93 " pdb=" N LEU V 94 " ideal model delta sigma weight residual 1.333 1.263 0.070 2.74e-02 1.33e+03 6.53e+00 bond pdb=" C ARG U 93 " pdb=" N LEU U 94 " ideal model delta sigma weight residual 1.333 1.263 0.069 2.74e-02 1.33e+03 6.39e+00 bond pdb=" C PHE E 336 " pdb=" N GLY E 337 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.46e-02 4.69e+03 4.26e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.08e+00 ... (remaining 50238 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.39: 1639 105.39 - 112.59: 25966 112.59 - 119.79: 16481 119.79 - 126.99: 23773 126.99 - 134.19: 1024 Bond angle restraints: 68883 Sorted by residual: angle pdb=" N LEU L 181 " pdb=" CA LEU L 181 " pdb=" C LEU L 181 " ideal model delta sigma weight residual 112.35 121.25 -8.90 1.34e+00 5.57e-01 4.42e+01 angle pdb=" N ALA E 339 " pdb=" CA ALA E 339 " pdb=" C ALA E 339 " ideal model delta sigma weight residual 111.30 104.37 6.93 1.43e+00 4.89e-01 2.35e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 108.58 101.83 6.75 1.44e+00 4.82e-01 2.20e+01 angle pdb=" N LYS E 238 " pdb=" CA LYS E 238 " pdb=" C LYS E 238 " ideal model delta sigma weight residual 112.92 118.56 -5.64 1.23e+00 6.61e-01 2.10e+01 angle pdb=" C ALA U 205 " pdb=" N ASN U 206 " pdb=" CA ASN U 206 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+01 ... (remaining 68878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 28039 35.06 - 70.12: 1111 70.12 - 105.19: 104 105.19 - 140.25: 6 140.25 - 175.31: 10 Dihedral angle restraints: 29270 sinusoidal: 12468 harmonic: 16802 Sorted by residual: dihedral pdb=" O4' U J 33 " pdb=" C1' U J 33 " pdb=" N1 U J 33 " pdb=" C2 U J 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.46 147.54 1 1.50e+01 4.44e-03 7.87e+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 52.53 147.47 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' U T 21 " pdb=" C1' U T 21 " pdb=" N1 U T 21 " pdb=" C2 U T 21 " ideal model delta sinusoidal sigma weight residual 200.00 63.24 136.76 1 1.50e+01 4.44e-03 7.37e+01 ... (remaining 29267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 7163 0.108 - 0.216: 335 0.216 - 0.324: 9 0.324 - 0.433: 1 0.433 - 0.541: 3 Chirality restraints: 7511 Sorted by residual: chirality pdb=" CB VAL X 199 " pdb=" CA VAL X 199 " pdb=" CG1 VAL X 199 " pdb=" CG2 VAL X 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CB VAL A 199 " pdb=" CA VAL A 199 " pdb=" CG1 VAL A 199 " pdb=" CG2 VAL A 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.18e+00 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 2.17 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 7508 not shown) Planarity restraints: 8618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 248 " 0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C SER F 248 " -0.072 2.00e-02 2.50e+03 pdb=" O SER F 248 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL F 249 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO A 270 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO X 269 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO X 270 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO X 270 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO X 270 " 0.042 5.00e-02 4.00e+02 ... (remaining 8615 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 635 2.62 - 3.19: 40569 3.19 - 3.76: 77693 3.76 - 4.33: 108202 4.33 - 4.90: 174557 Nonbonded interactions: 401656 Sorted by model distance: nonbonded pdb=" O ASN U 2 " pdb=" OD1 ASN U 2 " model vdw 2.049 3.040 nonbonded pdb=" O ASN V 2 " pdb=" OD1 ASN V 2 " model vdw 2.052 3.040 nonbonded pdb=" CD1 LEU L 181 " pdb=" CD PRO L 182 " model vdw 2.086 3.860 nonbonded pdb=" N1 DG K 42 " pdb=" O6 DG W 2 " model vdw 2.104 2.520 nonbonded pdb=" OG SER U 191 " pdb=" OD1 ASN U 194 " model vdw 2.214 2.440 ... (remaining 401651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'X' } 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 or (resid 14 and (name N or name CA or name C or name \ O or name CB )) or resid 15 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 51 or (resid 52 and (name N or \ name CA or name C or name O or name CB )) or resid 53 through 62 or (resid 63 an \ d (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 )) o \ r resid 69 through 76 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 93 or (resid 94 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 through 112 or ( \ resid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 \ through 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 na \ me O or name CB )) or resid 129 through 146 or (resid 147 and (name N or name CA \ or name C or name O or name CB )) or resid 148 through 157 or (resid 158 and (n \ ame N or name CA or name C or name O or name CB )) or resid 159 through 160 or ( \ resid 161 through 162 and (name N or name CA or name C or name O or name CB )) o \ r 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 \ name 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 (resi \ d 178 and (name N or name CA or name C or name O or name CB )) or resid 179 thro \ ugh 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) o \ r resid 193 through 197 or (resid 198 and (name N or name CA or name C or name O \ or name CB )) or resid 199 through 209 or (resid 210 and (name N or name CA or \ name 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 (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 239 through 240 and (name N or name CA or name C or name O or \ name 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 \ name CA or name C or name O or name CB )) or resid 278 through 281 or (resid 28 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 283 through \ 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or re \ sid 291 through 300 or (resid 301 and (name N or name CA or name C or name O or \ name 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 \ name CA or name C or name O or name CB )) or resid 315 through 319 or (resid 32 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 321 through \ 322)) } 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 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through 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 44 or ( \ resid 45 and (name N or name CA or name C or name O or name CB )) or resid 46 th \ rough 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) o \ r resid 85 through 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 nam \ e CA or name C or name O or name CB )) or resid 111 through 113 or (resid 114 th \ rough 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 139 or (resi \ d 140 and (name N or name CA or name C or name O or name CB )) or resid 141 thro \ ugh 155 or (resid 156 through 157 and (name N or name CA or name C or name O or \ name CB )) or resid 158 through 160 or (resid 161 through 162 and (name N or nam \ e 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 through 168 or (resid 16 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 170 through \ 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) or re \ sid 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) o \ r resid 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 217 or (resid 218 and (name N or name CA or name C or na \ me 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 231 and (name N or nam \ e CA or name C or name O or name CB )) or resid 244 through 245 or (resid 246 an \ d (name N or name CA or name C or name O or name CB )) or resid 247 through 270 \ or (resid 271 and (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 name C or na \ me O or name CB )) or resid 276 or (resid 277 and (name N or name CA or name C o \ r name O or name CB )) or resid 278 through 282 or (resid 283 and (name N or nam \ e 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 29 \ 1 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 name O or \ name CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or nam \ e CA or name C or name O or name CB )) or resid 304 through 306 or (resid 307 an \ d (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 (resid 324 and (name N or name CA or name C o \ r name O or name CB )) or resid 325 through 326 or (resid 327 through 328 and (n \ ame N or name CA or name C or name O or name CB )) or resid 329 or (resid 330 an \ d (name N or name CA or name C or name O or name CB )) or resid 331 through 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 231 and (name N or name CA or name \ C or name O or name CB )) or 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 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame 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 n \ ame 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 res \ id 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 (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 20 or (resid 321 and (name N or name CA or name C or name O or name CB )) or res \ id 322 through 323 or (resid 324 and (name N or name CA or name C or name O or n \ ame 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 (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 231 and (name N or name CA or name \ C or name O or name CB )) or 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 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame 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 n \ ame 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 res \ id 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 (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 20 or (resid 321 and (name N or name CA or name C or name O or name CB )) or res \ id 322 through 323 or (resid 324 and (name N or name CA or name C or name O or n \ ame 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 (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 231 and (name N or name CA or name \ C or name O or name CB )) or 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 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame 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 (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 2 \ 98 or (resid 299 and (name N or name CA or name C or name O or name CB )) or res \ id 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 (resid 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 320 o \ r (resid 321 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 22 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 \ (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 231 and (name N or name CA or name \ C or name O or name CB )) or 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 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame 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 n \ ame 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 res \ id 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 (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 23 or (resid 324 and (name N or name CA or name C or name O or name CB )) or res \ id 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 (name 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 231 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 44 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 (resid 277 and \ (name N or name CA or name C or name O or name CB )) or resid 278 through 282 o \ r (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 84 or (resid 285 and (name N or name CA or name C or name O or name CB )) or res \ id 286 through 290 or (resid 291 and (name N or name CA or name C or name O or n \ ame 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 3 \ 04 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 (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 329 o \ r (resid 330 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 31 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 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 'K' selection = chain 'Y' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'W' selection = chain 'Z' } 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: 11.180 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: 0.000 Extract box with map and model: 6.820 Check model and map are aligned: 0.700 Set scattering table: 0.420 Process input model: 128.930 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.350 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: 0.010 Load rotamer database and sin/cos tables:14.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.007 0.071 50243 Z= 0.487 Angle : 0.837 9.031 68883 Z= 0.481 Chirality : 0.052 0.541 7511 Planarity : 0.006 0.075 8618 Dihedral : 17.897 175.310 18796 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 0.58 % Allowed : 11.71 % Favored : 87.71 % 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: -3.03 (0.09), residues: 6156 helix: -2.28 (0.08), residues: 1977 sheet: -0.13 (0.15), residues: 1050 loop : -2.54 (0.09), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 174 HIS 0.010 0.002 HIS S 3 PHE 0.022 0.002 PHE L 152 TYR 0.022 0.002 TYR P 271 ARG 0.010 0.001 ARG S 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 468 time to evaluate : 5.426 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: B 284 PHE cc_start: 0.7827 (m-80) cc_final: 0.7590 (m-80) REVERT: C 221 ASP cc_start: 0.8104 (m-30) cc_final: 0.7748 (t0) REVERT: C 223 GLN cc_start: 0.6666 (mp10) cc_final: 0.5715 (mt0) REVERT: C 277 LEU cc_start: 0.3769 (pp) cc_final: 0.3538 (mm) REVERT: H 167 GLN cc_start: 0.8183 (tp40) cc_final: 0.7881 (tp40) REVERT: I 21 MET cc_start: 0.2383 (ptt) cc_final: 0.1537 (tpp) REVERT: L 171 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8249 (ptpp) REVERT: L 174 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7926 (ttp-170) REVERT: M 197 GLU cc_start: 0.7720 (tp30) cc_final: 0.7480 (tp30) REVERT: M 219 ILE cc_start: 0.8285 (mp) cc_final: 0.8021 (mp) REVERT: P 46 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7656 (mt-10) REVERT: R 299 LYS cc_start: 0.8807 (ptmt) cc_final: 0.8604 (mmmt) REVERT: A 207 ARG cc_start: 0.8228 (ptp-110) cc_final: 0.7878 (ptm-80) REVERT: A 241 GLN cc_start: 0.8319 (tt0) cc_final: 0.8004 (tt0) REVERT: X 253 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7706 (tp40) outliers start: 25 outliers final: 17 residues processed: 487 average time/residue: 1.8866 time to fit residues: 1109.7243 Evaluate side-chains 274 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 257 time to evaluate : 5.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 211 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 529 optimal weight: 2.9990 chunk 475 optimal weight: 30.0000 chunk 263 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 491 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 365 optimal weight: 0.9980 chunk 569 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 82 ASN B 129 GLN B 196 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 127 ASN D 75 ASN D 291 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 241 GLN G 72 GLN H 75 ASN I 3 HIS I 35 GLN I 99 GLN I 165 GLN L 129 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 GLN N 120 GLN ** N 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 223 GLN P 291 GLN Q 120 GLN Q 291 GLN R 120 GLN ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 HIS ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 HIS U 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 230 HIS X 64 GLN X 68 HIS X 177 GLN ** X 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 230 HIS X 253 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 50243 Z= 0.199 Angle : 0.541 9.586 68883 Z= 0.292 Chirality : 0.040 0.155 7511 Planarity : 0.004 0.056 8618 Dihedral : 17.096 178.558 9196 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.16 % Allowed : 16.56 % Favored : 81.28 % 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: -1.42 (0.10), residues: 6156 helix: -0.02 (0.11), residues: 1993 sheet: 0.29 (0.15), residues: 1041 loop : -2.06 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 174 HIS 0.013 0.001 HIS X 188 PHE 0.013 0.001 PHE A 232 TYR 0.014 0.002 TYR R 285 ARG 0.012 0.001 ARG L 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 311 time to evaluate : 5.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8825 (m) cc_final: 0.8382 (p) REVERT: B 284 PHE cc_start: 0.7760 (m-80) cc_final: 0.7459 (m-80) REVERT: C 87 ASP cc_start: 0.7338 (p0) cc_final: 0.6795 (t0) REVERT: C 221 ASP cc_start: 0.8152 (m-30) cc_final: 0.7770 (t0) REVERT: C 223 GLN cc_start: 0.6682 (mp10) cc_final: 0.5654 (mt0) REVERT: H 233 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8107 (mm) REVERT: I 21 MET cc_start: 0.2348 (ptt) cc_final: 0.1474 (mtt) REVERT: L 171 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8119 (ptpt) REVERT: L 174 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7883 (ttp-170) REVERT: M 264 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8283 (tm) REVERT: U 127 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: V 46 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: V 209 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8757 (mmmm) REVERT: A 59 ARG cc_start: 0.6608 (mmp80) cc_final: 0.5196 (mmt90) REVERT: A 81 ASN cc_start: 0.6646 (p0) cc_final: 0.6125 (p0) REVERT: A 207 ARG cc_start: 0.8210 (ptp-110) cc_final: 0.7899 (ptm-80) REVERT: A 258 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8150 (mtp180) REVERT: X 253 GLN cc_start: 0.7527 (tp40) cc_final: 0.6772 (tp40) outliers start: 93 outliers final: 34 residues processed: 381 average time/residue: 1.6399 time to fit residues: 778.7889 Evaluate side-chains 295 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 167 GLN Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain X residue 81 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 316 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 473 optimal weight: 0.7980 chunk 387 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 570 optimal weight: 30.0000 chunk 616 optimal weight: 0.0970 chunk 508 optimal weight: 4.9990 chunk 565 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 457 optimal weight: 5.9990 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN M 140 HIS ** N 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN V 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN A 68 HIS A 200 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 50243 Z= 0.263 Angle : 0.542 11.675 68883 Z= 0.290 Chirality : 0.040 0.178 7511 Planarity : 0.004 0.063 8618 Dihedral : 16.976 179.341 9179 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.62 % Allowed : 18.07 % Favored : 79.31 % 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: -0.71 (0.10), residues: 6156 helix: 0.96 (0.11), residues: 2004 sheet: 0.44 (0.15), residues: 1048 loop : -1.84 (0.10), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 311 HIS 0.006 0.001 HIS X 188 PHE 0.013 0.001 PHE C 95 TYR 0.022 0.002 TYR C 114 ARG 0.010 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 273 time to evaluate : 5.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8741 (m) cc_final: 0.8412 (p) REVERT: B 284 PHE cc_start: 0.7758 (m-80) cc_final: 0.7526 (m-80) REVERT: C 87 ASP cc_start: 0.7266 (p0) cc_final: 0.6665 (t0) REVERT: C 221 ASP cc_start: 0.8158 (m-30) cc_final: 0.7827 (t0) REVERT: C 223 GLN cc_start: 0.6531 (mp10) cc_final: 0.5556 (mt0) REVERT: D 208 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7488 (t70) REVERT: E 60 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8752 (ttpt) REVERT: H 34 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7261 (p0) REVERT: H 314 ARG cc_start: 0.8293 (mmt90) cc_final: 0.7672 (mpp80) REVERT: I 21 MET cc_start: 0.2354 (ptt) cc_final: 0.1447 (tpp) REVERT: L 171 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8194 (ptpt) REVERT: L 174 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7871 (ttp-170) REVERT: L 321 PHE cc_start: 0.6955 (p90) cc_final: 0.6101 (t80) REVERT: M 264 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8196 (tm) REVERT: R 314 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.7071 (mpp80) REVERT: U 37 MET cc_start: 0.8383 (mtp) cc_final: 0.8167 (mtp) REVERT: U 127 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: V 46 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: V 209 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8715 (mmmm) REVERT: A 59 ARG cc_start: 0.5976 (mmp80) cc_final: 0.5334 (mmt90) REVERT: A 207 ARG cc_start: 0.8309 (ptp-110) cc_final: 0.7911 (ptm-80) REVERT: A 208 GLU cc_start: 0.8222 (tp30) cc_final: 0.7875 (tp30) REVERT: A 216 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8799 (mmmm) REVERT: X 65 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7696 (tm) outliers start: 113 outliers final: 54 residues processed: 363 average time/residue: 1.5135 time to fit residues: 691.0665 Evaluate side-chains 299 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 237 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 127 ASN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 GLN Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 202 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 563 optimal weight: 10.0000 chunk 428 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 383 optimal weight: 4.9990 chunk 572 optimal weight: 30.0000 chunk 606 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 542 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN B 69 GLN B 82 ASN B 196 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN D 208 HIS ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN F 120 GLN F 127 ASN G 167 GLN H 75 ASN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 ASN M 140 HIS N 291 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN R 140 HIS ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN U 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN A 83 HIS A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 50243 Z= 0.565 Angle : 0.696 15.710 68883 Z= 0.369 Chirality : 0.046 0.264 7511 Planarity : 0.005 0.059 8618 Dihedral : 17.055 178.813 9179 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.55 % Allowed : 18.86 % Favored : 77.59 % 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: -0.70 (0.10), residues: 6156 helix: 0.96 (0.11), residues: 2001 sheet: 0.35 (0.15), residues: 1036 loop : -1.78 (0.10), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 174 HIS 0.011 0.002 HIS G 256 PHE 0.025 0.002 PHE C 95 TYR 0.024 0.002 TYR X 179 ARG 0.008 0.001 ARG X 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 261 time to evaluate : 4.509 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: B 284 PHE cc_start: 0.7883 (m-80) cc_final: 0.7674 (m-80) REVERT: C 223 GLN cc_start: 0.6430 (mp10) cc_final: 0.5390 (mt0) REVERT: C 285 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: C 301 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8165 (ttmm) REVERT: E 283 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: H 242 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8183 (ptmm) REVERT: H 314 ARG cc_start: 0.8428 (mmt90) cc_final: 0.7840 (mpp80) REVERT: I 21 MET cc_start: 0.3011 (ptt) cc_final: 0.1785 (tpp) REVERT: L 171 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8242 (ptpt) REVERT: L 174 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8068 (ttp-170) REVERT: L 321 PHE cc_start: 0.7121 (p90) cc_final: 0.5947 (t80) REVERT: M 45 ARG cc_start: 0.6511 (pmt170) cc_final: 0.6189 (pmt170) REVERT: U 37 MET cc_start: 0.8423 (mtp) cc_final: 0.8218 (mtp) REVERT: U 127 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: V 46 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: V 116 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6997 (tpp-160) REVERT: A 65 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7657 (mp) REVERT: A 207 ARG cc_start: 0.8268 (ptp-110) cc_final: 0.7905 (ptm-80) REVERT: A 241 GLN cc_start: 0.8238 (tt0) cc_final: 0.7817 (tt0) REVERT: X 59 ARG cc_start: 0.6897 (mtt180) cc_final: 0.6149 (mmt180) outliers start: 153 outliers final: 72 residues processed: 390 average time/residue: 1.6133 time to fit residues: 787.8365 Evaluate side-chains 312 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 233 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 116 ARG Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 246 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 504 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 451 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 517 optimal weight: 0.7980 chunk 418 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 309 optimal weight: 0.9980 chunk 543 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 241 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50243 Z= 0.167 Angle : 0.522 10.637 68883 Z= 0.277 Chirality : 0.039 0.218 7511 Planarity : 0.003 0.049 8618 Dihedral : 16.868 178.864 9177 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.27 % Allowed : 20.53 % Favored : 77.20 % 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: -0.21 (0.11), residues: 6156 helix: 1.62 (0.12), residues: 1974 sheet: 0.39 (0.15), residues: 1085 loop : -1.59 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 174 HIS 0.004 0.001 HIS X 83 PHE 0.015 0.001 PHE L 152 TYR 0.022 0.001 TYR Q 114 ARG 0.007 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 268 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8695 (m) cc_final: 0.8444 (p) REVERT: B 284 PHE cc_start: 0.7869 (m-80) cc_final: 0.7629 (m-80) REVERT: C 223 GLN cc_start: 0.6337 (mp10) cc_final: 0.5372 (mt0) REVERT: C 301 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7957 (ttmm) REVERT: H 34 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7459 (OUTLIER) REVERT: I 21 MET cc_start: 0.2947 (ptt) cc_final: 0.1781 (tpp) REVERT: L 161 MET cc_start: 0.6745 (pmm) cc_final: 0.6254 (pmm) REVERT: L 171 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8153 (ptpt) REVERT: L 174 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8046 (ttp-170) REVERT: L 321 PHE cc_start: 0.7078 (p90) cc_final: 0.6039 (t80) REVERT: M 264 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8203 (tm) REVERT: N 76 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8636 (mt) REVERT: U 127 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: V 46 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: V 209 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8831 (mmmm) REVERT: A 207 ARG cc_start: 0.8239 (ptp-110) cc_final: 0.7843 (ptm-80) REVERT: A 216 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8852 (mmmm) REVERT: A 241 GLN cc_start: 0.8174 (tt0) cc_final: 0.7831 (tt0) REVERT: X 59 ARG cc_start: 0.6549 (mtt180) cc_final: 0.5930 (mmt180) REVERT: X 237 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.7956 (p0) outliers start: 98 outliers final: 42 residues processed: 350 average time/residue: 1.5505 time to fit residues: 678.8059 Evaluate side-chains 291 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 237 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 203 optimal weight: 10.0000 chunk 545 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 355 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 606 optimal weight: 9.9990 chunk 503 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN R 140 HIS ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50243 Z= 0.234 Angle : 0.539 13.803 68883 Z= 0.283 Chirality : 0.040 0.181 7511 Planarity : 0.004 0.048 8618 Dihedral : 16.794 178.913 9177 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.41 % Allowed : 20.90 % Favored : 76.69 % 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: 6156 helix: 1.73 (0.12), residues: 1987 sheet: 0.50 (0.15), residues: 1082 loop : -1.53 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 147 HIS 0.004 0.001 HIS G 256 PHE 0.014 0.001 PHE L 152 TYR 0.026 0.001 TYR Q 114 ARG 0.010 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 258 time to evaluate : 5.384 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: B 284 PHE cc_start: 0.7939 (m-80) cc_final: 0.7713 (m-80) REVERT: C 223 GLN cc_start: 0.6295 (mp10) cc_final: 0.5398 (mt0) REVERT: C 301 LYS cc_start: 0.8448 (mmtm) cc_final: 0.8009 (ttmm) REVERT: G 58 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7950 (ttmm) REVERT: H 34 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7455 (p0) REVERT: I 21 MET cc_start: 0.3226 (ptt) cc_final: 0.1749 (tpp) REVERT: L 174 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8093 (mtp180) REVERT: L 290 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8826 (pp) REVERT: L 321 PHE cc_start: 0.7133 (p90) cc_final: 0.6111 (t80) REVERT: M 221 ASP cc_start: 0.7831 (t0) cc_final: 0.7442 (t70) REVERT: M 264 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8182 (tm) REVERT: N 76 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8634 (mt) REVERT: R 314 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7216 (mpp80) REVERT: U 127 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: V 46 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: V 190 MET cc_start: 0.8126 (mtm) cc_final: 0.7868 (ptp) REVERT: V 209 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8864 (mmmm) REVERT: A 65 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 81 ASN cc_start: 0.7642 (p0) cc_final: 0.6984 (p0) REVERT: A 207 ARG cc_start: 0.8242 (ptp-110) cc_final: 0.7876 (ptm-80) REVERT: A 211 PHE cc_start: 0.8617 (m-80) cc_final: 0.8410 (m-80) REVERT: A 216 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8902 (mmmm) REVERT: A 241 GLN cc_start: 0.8224 (tt0) cc_final: 0.7791 (tt0) REVERT: X 59 ARG cc_start: 0.6630 (mtt180) cc_final: 0.6001 (mmt180) outliers start: 104 outliers final: 60 residues processed: 348 average time/residue: 1.5742 time to fit residues: 694.3322 Evaluate side-chains 308 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 240 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 117 MET Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 81 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 584 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 443 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 chunk 510 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 chunk 604 optimal weight: 7.9990 chunk 378 optimal weight: 0.3980 chunk 368 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 HIS L 129 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 50243 Z= 0.344 Angle : 0.583 12.634 68883 Z= 0.307 Chirality : 0.042 0.198 7511 Planarity : 0.004 0.052 8618 Dihedral : 16.808 179.714 9177 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.76 % Allowed : 20.85 % Favored : 76.39 % 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: -0.09 (0.11), residues: 6156 helix: 1.68 (0.12), residues: 1999 sheet: 0.56 (0.16), residues: 1067 loop : -1.54 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 147 HIS 0.007 0.001 HIS G 256 PHE 0.015 0.001 PHE C 95 TYR 0.026 0.002 TYR Q 114 ARG 0.008 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 248 time to evaluate : 5.383 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: C 223 GLN cc_start: 0.6337 (mp10) cc_final: 0.5391 (mt0) REVERT: C 301 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8145 (ttmm) REVERT: H 34 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7631 (p0) REVERT: I 21 MET cc_start: 0.3568 (ptt) cc_final: 0.2120 (tpp) REVERT: L 171 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8195 (ptpt) REVERT: L 290 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8785 (pp) REVERT: L 321 PHE cc_start: 0.7022 (p90) cc_final: 0.6038 (t80) REVERT: M 264 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8179 (tm) REVERT: N 76 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8595 (mt) REVERT: U 127 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: V 46 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: V 209 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8778 (mmmm) REVERT: A 81 ASN cc_start: 0.7624 (p0) cc_final: 0.6980 (p0) REVERT: A 207 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.7886 (ptm-80) REVERT: A 211 PHE cc_start: 0.8690 (m-80) cc_final: 0.8477 (m-80) REVERT: A 241 GLN cc_start: 0.8301 (tt0) cc_final: 0.7877 (tt0) REVERT: X 59 ARG cc_start: 0.6759 (mtt180) cc_final: 0.6065 (mmt180) outliers start: 119 outliers final: 73 residues processed: 351 average time/residue: 1.6103 time to fit residues: 707.7029 Evaluate side-chains 313 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 233 time to evaluate : 5.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 117 MET Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 237 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 373 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 384 optimal weight: 2.9990 chunk 411 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 475 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN F 208 HIS ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 50243 Z= 0.169 Angle : 0.521 17.168 68883 Z= 0.273 Chirality : 0.039 0.204 7511 Planarity : 0.003 0.044 8618 Dihedral : 16.692 178.752 9177 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.95 % Allowed : 21.74 % Favored : 76.32 % 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: 0.10 (0.11), residues: 6156 helix: 1.94 (0.12), residues: 1988 sheet: 0.50 (0.15), residues: 1143 loop : -1.47 (0.11), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 147 HIS 0.004 0.001 HIS X 83 PHE 0.011 0.001 PHE U 212 TYR 0.024 0.001 TYR Q 114 ARG 0.009 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 263 time to evaluate : 5.158 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: C 223 GLN cc_start: 0.6261 (mp10) cc_final: 0.5383 (mt0) REVERT: C 301 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8019 (ttmm) REVERT: H 34 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7542 (p0) REVERT: I 21 MET cc_start: 0.3541 (ptt) cc_final: 0.2470 (tpp) REVERT: L 290 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8766 (pp) REVERT: L 321 PHE cc_start: 0.6955 (p90) cc_final: 0.6071 (t80) REVERT: M 221 ASP cc_start: 0.7737 (t0) cc_final: 0.7512 (t70) REVERT: M 264 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8245 (tm) REVERT: N 76 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8542 (mt) REVERT: Q 80 ASP cc_start: 0.7992 (m-30) cc_final: 0.7709 (t0) REVERT: R 314 ARG cc_start: 0.7202 (mpp80) cc_final: 0.6979 (mtm-85) REVERT: U 190 MET cc_start: 0.8451 (mtp) cc_final: 0.8162 (mtp) REVERT: V 46 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: V 209 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8895 (mmmm) REVERT: A 81 ASN cc_start: 0.7591 (p0) cc_final: 0.6954 (p0) REVERT: A 207 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.7983 (ptm-80) REVERT: A 241 GLN cc_start: 0.8276 (tt0) cc_final: 0.7842 (tt0) REVERT: A 259 TYR cc_start: 0.8692 (m-80) cc_final: 0.8489 (m-80) REVERT: X 59 ARG cc_start: 0.6637 (mtt180) cc_final: 0.5915 (mmt180) REVERT: X 224 ARG cc_start: 0.8156 (mmt-90) cc_final: 0.7837 (tpp-160) REVERT: X 237 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.7928 (p0) outliers start: 84 outliers final: 54 residues processed: 334 average time/residue: 1.5791 time to fit residues: 661.2119 Evaluate side-chains 309 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 208 HIS Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 83 ASP Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 237 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 549 optimal weight: 0.4980 chunk 578 optimal weight: 50.0000 chunk 528 optimal weight: 5.9990 chunk 563 optimal weight: 9.9990 chunk 338 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 442 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 508 optimal weight: 2.9990 chunk 532 optimal weight: 50.0000 chunk 561 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS M 140 HIS ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 HIS ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN R 140 HIS ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN U 208 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 50243 Z= 0.352 Angle : 0.589 12.789 68883 Z= 0.308 Chirality : 0.042 0.226 7511 Planarity : 0.004 0.054 8618 Dihedral : 16.717 179.673 9177 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.27 % Allowed : 21.85 % Favored : 75.88 % 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: 0.04 (0.11), residues: 6156 helix: 1.86 (0.12), residues: 1988 sheet: 0.54 (0.15), residues: 1105 loop : -1.49 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 174 HIS 0.006 0.001 HIS L 305 PHE 0.016 0.001 PHE I 44 TYR 0.026 0.002 TYR Q 114 ARG 0.011 0.000 ARG X 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 251 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: C 32 GLN cc_start: 0.7794 (pm20) cc_final: 0.7471 (pm20) REVERT: C 223 GLN cc_start: 0.6362 (mp10) cc_final: 0.5449 (mt0) REVERT: C 301 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8175 (ttmm) REVERT: H 34 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7743 (p0) REVERT: I 21 MET cc_start: 0.3845 (ptt) cc_final: 0.2116 (tpp) REVERT: L 171 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8179 (ptpt) REVERT: L 290 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8746 (pp) REVERT: L 321 PHE cc_start: 0.6719 (p90) cc_final: 0.5843 (t80) REVERT: M 221 ASP cc_start: 0.7792 (t0) cc_final: 0.7584 (t70) REVERT: M 264 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8193 (tm) REVERT: N 76 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8581 (mt) REVERT: R 338 GLU cc_start: 0.3257 (OUTLIER) cc_final: 0.1348 (mp0) REVERT: V 46 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: V 209 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8925 (mmmm) REVERT: A 65 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 81 ASN cc_start: 0.7547 (p0) cc_final: 0.6902 (p0) REVERT: A 207 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7842 (ptm-80) REVERT: A 241 GLN cc_start: 0.8295 (tt0) cc_final: 0.7786 (tt0) REVERT: X 59 ARG cc_start: 0.6899 (mtt180) cc_final: 0.6083 (mmt180) REVERT: X 222 ARG cc_start: 0.6051 (tpp-160) cc_final: 0.5782 (tpp-160) outliers start: 98 outliers final: 69 residues processed: 336 average time/residue: 1.5515 time to fit residues: 657.0386 Evaluate side-chains 316 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 239 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 338 GLU Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 73 ASP Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 237 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 369 optimal weight: 4.9990 chunk 595 optimal weight: 30.0000 chunk 363 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 413 optimal weight: 2.9990 chunk 624 optimal weight: 20.0000 chunk 574 optimal weight: 0.0000 chunk 497 optimal weight: 0.0770 chunk 51 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN L 121 HIS ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** U 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 50243 Z= 0.168 Angle : 0.531 15.075 68883 Z= 0.276 Chirality : 0.039 0.256 7511 Planarity : 0.003 0.046 8618 Dihedral : 16.635 178.964 9177 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.62 % Allowed : 22.78 % Favored : 75.60 % 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: 0.20 (0.11), residues: 6156 helix: 2.04 (0.12), residues: 1988 sheet: 0.50 (0.15), residues: 1147 loop : -1.40 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 174 HIS 0.007 0.001 HIS L 121 PHE 0.015 0.001 PHE I 44 TYR 0.024 0.001 TYR Q 114 ARG 0.009 0.000 ARG X 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 258 time to evaluate : 5.682 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: C 32 GLN cc_start: 0.7696 (pm20) cc_final: 0.7401 (pm20) REVERT: C 223 GLN cc_start: 0.6272 (mp10) cc_final: 0.5421 (mt0) REVERT: C 301 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8081 (ttmm) REVERT: H 34 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7576 (p0) REVERT: H 314 ARG cc_start: 0.8366 (mmt90) cc_final: 0.7878 (mpp80) REVERT: I 21 MET cc_start: 0.3912 (ptt) cc_final: 0.2040 (tpp) REVERT: L 171 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8181 (ptpt) REVERT: L 290 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8750 (pp) REVERT: L 321 PHE cc_start: 0.6762 (p90) cc_final: 0.6036 (t80) REVERT: M 264 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8249 (tm) REVERT: N 76 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8514 (mt) REVERT: Q 80 ASP cc_start: 0.8012 (m-30) cc_final: 0.7745 (t0) REVERT: R 338 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.1535 (mp0) REVERT: S 1 MET cc_start: 0.2603 (mtm) cc_final: 0.0193 (ppp) REVERT: U 190 MET cc_start: 0.8469 (mtp) cc_final: 0.8180 (mtp) REVERT: V 46 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: V 209 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8855 (mmmm) REVERT: A 65 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7933 (mp) REVERT: A 81 ASN cc_start: 0.7592 (p0) cc_final: 0.6953 (p0) REVERT: A 207 ARG cc_start: 0.8266 (ptp-110) cc_final: 0.7982 (ptm-80) REVERT: A 241 GLN cc_start: 0.8291 (tt0) cc_final: 0.7778 (tt0) REVERT: X 59 ARG cc_start: 0.6799 (mtt180) cc_final: 0.5968 (mmt180) REVERT: X 224 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7917 (tpp-160) REVERT: X 237 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.7938 (p0) outliers start: 70 outliers final: 55 residues processed: 320 average time/residue: 1.5875 time to fit residues: 638.2247 Evaluate side-chains 314 residues out of total 5025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 5.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 140 HIS Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain R residue 338 GLU Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 49 SER Chi-restraints excluded: chain V residue 83 ASP Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 237 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 395 optimal weight: 0.6980 chunk 529 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 458 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 498 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 511 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 208 HIS ** S 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** U 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.083948 restraints weight = 115537.166| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.72 r_work: 0.3060 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50243 Z= 0.192 Angle : 0.533 14.759 68883 Z= 0.277 Chirality : 0.039 0.326 7511 Planarity : 0.003 0.043 8618 Dihedral : 16.588 178.928 9175 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.62 % Allowed : 22.78 % Favored : 75.60 % 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: 0.26 (0.11), residues: 6156 helix: 2.08 (0.12), residues: 1990 sheet: 0.54 (0.15), residues: 1147 loop : -1.36 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 174 HIS 0.008 0.001 HIS L 121 PHE 0.025 0.001 PHE R 14 TYR 0.025 0.001 TYR Q 114 ARG 0.010 0.000 ARG R 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14379.81 seconds wall clock time: 256 minutes 58.18 seconds (15418.18 seconds total)