Starting phenix.real_space_refine on Mon Mar 25 07:56:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/03_2024/7elm_31185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/03_2024/7elm_31185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/03_2024/7elm_31185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/03_2024/7elm_31185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/03_2024/7elm_31185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elm_31185/03_2024/7elm_31185.pdb" } resolution = 2.88 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 46 5.16 5 C 29098 2.51 5 N 8735 2.21 5 O 9402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "K GLU 220": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M GLU 224": "OE1" <-> "OE2" Residue "M GLU 321": "OE1" <-> "OE2" Residue "N GLU 38": "OE1" <-> "OE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 340": "OE1" <-> "OE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "P GLU 38": "OE1" <-> "OE2" Residue "P TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "Q GLU 169": "OE1" <-> "OE2" Residue "Q GLU 283": "OE1" <-> "OE2" Residue "R GLU 15": "OE1" <-> "OE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "R GLU 197": "OE1" <-> "OE2" Residue "S GLU 14": "OE1" <-> "OE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S GLU 124": "OE1" <-> "OE2" Residue "S GLU 125": "OE1" <-> "OE2" Residue "S PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 169": "OE1" <-> "OE2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 157": "OE1" <-> "OE2" Residue "U GLU 158": "OE1" <-> "OE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 157": "OE1" <-> "OE2" Residue "V GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47399 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 2015 Classifications: {'peptide': 417} Incomplete info: {'backbone_only': 298, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 392} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1377 Unresolved non-hydrogen angles: 1978 Unresolved non-hydrogen dihedrals: 900 Unresolved non-hydrogen chiralities: 378 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 20, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 8, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 743 Chain: "B" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2204 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 128 Chain: "C" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2139 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2531 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2590 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 324} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2577 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2517 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2490 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "K" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2065 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 301, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1400 Unresolved non-hydrogen angles: 2015 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 380 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 21, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 10, 'HIS:plan': 11, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 772 Chain: "I" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2321 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2227 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2565 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "O" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2562 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2581 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2529 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1431 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 Conformer: "B" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 bond proxies already assigned to first conformer: 1462 Chain: "U" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "V" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "J" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 15, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 35} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen 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': 14, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 24, 'rna3p': 35} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 24.91, per 1000 atoms: 0.53 Number of scatterers: 47399 At special positions: 0 Unit cell: (166.501, 160.056, 236.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 118 15.00 O 9402 8.00 N 8735 7.00 C 29098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.74 Conformation dependent library (CDL) restraints added in 8.9 seconds 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10324 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 93 sheets defined 33.5% alpha, 20.7% beta 12 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 15.24 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 removed outlier: 3.615A pdb=" N SER A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 51 through 60 removed outlier: 4.172A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.611A pdb=" N ILE A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.875A pdb=" N SER A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.958A pdb=" N SER A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.612A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.520A pdb=" N ARG A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.235A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.471A pdb=" N GLY A 292 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.778A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 343 removed outlier: 5.394A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.522A pdb=" N GLN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.066A pdb=" N VAL A 387 " --> pdb=" O TRP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 432 removed outlier: 3.918A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.998A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.605A pdb=" N LEU B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.995A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 121' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.559A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.971A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.832A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.592A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.766A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.512A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.593A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.517A pdb=" N LEU F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.513A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.618A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 63 through 72 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.575A pdb=" N ARG H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'K' and resid 15 through 29 removed outlier: 3.786A pdb=" N SER K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 46 removed outlier: 3.931A pdb=" N LYS K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 60 removed outlier: 4.138A pdb=" N ASP K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 124 removed outlier: 4.086A pdb=" N SER K 122 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN K 124 " --> pdb=" O PHE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 134 Processing helix chain 'K' and resid 140 through 146 removed outlier: 4.145A pdb=" N SER K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 163 removed outlier: 3.972A pdb=" N THR K 163 " --> pdb=" O PHE K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 176 removed outlier: 3.744A pdb=" N ALA K 175 " --> pdb=" O HIS K 172 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS K 176 " --> pdb=" O SER K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 176' Processing helix chain 'K' and resid 195 through 211 Processing helix chain 'K' and resid 212 through 224 Processing helix chain 'K' and resid 282 through 287 removed outlier: 3.934A pdb=" N PHE K 287 " --> pdb=" O HIS K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 292 removed outlier: 4.423A pdb=" N GLY K 292 " --> pdb=" O HIS K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 307 removed outlier: 3.558A pdb=" N LEU K 307 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 342 removed outlier: 4.680A pdb=" N ARG K 320 " --> pdb=" O PHE K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 363 Processing helix chain 'K' and resid 372 through 376 Processing helix chain 'K' and resid 383 through 399 removed outlier: 3.841A pdb=" N VAL K 387 " --> pdb=" O TRP K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 407 Processing helix chain 'K' and resid 408 through 432 removed outlier: 4.022A pdb=" N ALA K 412 " --> pdb=" O SER K 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.591A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 removed outlier: 3.784A pdb=" N ALA I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 removed outlier: 4.037A pdb=" N LEU I 112 " --> pdb=" O ASN I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 131 Processing helix chain 'I' and resid 132 through 136 removed outlier: 3.801A pdb=" N VAL I 135 " --> pdb=" O PRO I 132 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA I 136 " --> pdb=" O ASP I 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 132 through 136' Processing helix chain 'L' and resid 33 through 48 removed outlier: 4.067A pdb=" N PHE L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.510A pdb=" N LEU L 52 " --> pdb=" O GLY L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 121 removed outlier: 4.000A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS L 121 " --> pdb=" O GLY L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 116 through 121' Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 165 through 178 Processing helix chain 'L' and resid 189 through 201 Processing helix chain 'L' and resid 207 through 214 removed outlier: 3.540A pdb=" N ASP L 211 " --> pdb=" O ALA L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.605A pdb=" N VAL L 295 " --> pdb=" O PRO L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 3.993A pdb=" N LEU L 301 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU L 302 " --> pdb=" O SER L 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 36 removed outlier: 3.550A pdb=" N SER M 36 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 129 removed outlier: 3.507A pdb=" N ARG M 115 " --> pdb=" O ASP M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 144 Processing helix chain 'M' and resid 189 through 204 Processing helix chain 'M' and resid 256 through 265 Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 319 through 333 Processing helix chain 'N' and resid 32 through 36 removed outlier: 3.780A pdb=" N SER N 36 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 73 removed outlier: 3.584A pdb=" N SER N 73 " --> pdb=" O ALA N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 129 Processing helix chain 'N' and resid 131 through 144 Processing helix chain 'N' and resid 189 through 204 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 303 through 313 Processing helix chain 'N' and resid 319 through 333 Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.913A pdb=" N SER O 36 " --> pdb=" O ARG O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.598A pdb=" N ARG O 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 removed outlier: 3.567A pdb=" N SER O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 129 Processing helix chain 'O' and resid 131 through 144 Processing helix chain 'O' and resid 189 through 204 Processing helix chain 'O' and resid 256 through 265 Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 319 through 333 Processing helix chain 'P' and resid 32 through 36 removed outlier: 3.677A pdb=" N SER P 36 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 72 removed outlier: 3.847A pdb=" N LEU P 67 " --> pdb=" O ASP P 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP P 68 " --> pdb=" O PRO P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 129 Processing helix chain 'P' and resid 131 through 144 Processing helix chain 'P' and resid 189 through 204 Processing helix chain 'P' and resid 256 through 265 Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 319 through 333 Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.594A pdb=" N SER Q 36 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.765A pdb=" N SER Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 129 Processing helix chain 'Q' and resid 131 through 144 Processing helix chain 'Q' and resid 189 through 204 Processing helix chain 'Q' and resid 256 through 265 Processing helix chain 'Q' and resid 303 through 313 Processing helix chain 'Q' and resid 319 through 333 Processing helix chain 'R' and resid 32 through 36 removed outlier: 3.511A pdb=" N SER R 36 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 62 removed outlier: 4.002A pdb=" N ARG R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 72 Processing helix chain 'R' and resid 111 through 129 Processing helix chain 'R' and resid 131 through 144 Processing helix chain 'R' and resid 189 through 204 Processing helix chain 'R' and resid 256 through 265 Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'R' and resid 319 through 333 Processing helix chain 'S' and resid 16 through 36 Processing helix chain 'S' and resid 63 through 72 removed outlier: 3.952A pdb=" N ALA S 72 " --> pdb=" O ARG S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 3.990A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS S 120 " --> pdb=" O LEU S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 131 Processing helix chain 'S' and resid 132 through 136 removed outlier: 3.772A pdb=" N VAL S 135 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA S 136 " --> pdb=" O ASP S 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 132 through 136' Processing helix chain 'U' and resid 47 through 70 removed outlier: 3.682A pdb=" N PHE U 55 " --> pdb=" O VAL U 51 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 136 Processing helix chain 'U' and resid 140 through 147 removed outlier: 3.549A pdb=" N ILE U 143 " --> pdb=" O LEU U 140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU U 147 " --> pdb=" O THR U 144 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 Processing helix chain 'U' and resid 180 through 188 Processing helix chain 'U' and resid 191 through 197 Processing helix chain 'U' and resid 198 through 200 No H-bonds generated for 'chain 'U' and resid 198 through 200' Processing helix chain 'U' and resid 211 through 222 Processing helix chain 'V' and resid 47 through 70 removed outlier: 3.683A pdb=" N PHE V 55 " --> pdb=" O VAL V 51 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP V 57 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 136 Processing helix chain 'V' and resid 140 through 147 removed outlier: 3.550A pdb=" N ILE V 143 " --> pdb=" O LEU V 140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU V 147 " --> pdb=" O THR V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 168 Processing helix chain 'V' and resid 180 through 188 Processing helix chain 'V' and resid 191 through 197 Processing helix chain 'V' and resid 198 through 200 No H-bonds generated for 'chain 'V' and resid 198 through 200' Processing helix chain 'V' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 removed outlier: 7.140A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 182 removed outlier: 5.227A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 280 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 removed outlier: 4.050A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG B 218 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.553A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 removed outlier: 5.038A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.502A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.830A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 49 Processing sheet with id=AB7, first strand: chain 'D' and resid 266 through 268 Processing sheet with id=AB8, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.627A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 108 through 109 Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.521A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.816A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER E 243 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.594A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 108 through 109 Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.908A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 45 through 51 removed outlier: 7.482A pdb=" N SER F 243 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR F 78 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD1, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD2, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.983A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD5, first strand: chain 'G' and resid 44 through 50 removed outlier: 7.520A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD7, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.602A pdb=" N VAL G 288 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.783A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.915A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.277A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.277A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N HIS U 26 " --> pdb=" O THR U 41 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR U 41 " --> pdb=" O HIS U 26 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP U 28 " --> pdb=" O ILE U 39 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE U 39 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU U 30 " --> pdb=" O MET U 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE5, first strand: chain 'K' and resid 178 through 181 Processing sheet with id=AE6, first strand: chain 'K' and resid 178 through 181 removed outlier: 7.276A pdb=" N PHE L 279 " --> pdb=" O ALA L 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA L 257 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU L 281 " --> pdb=" O TYR L 255 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR L 255 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU L 283 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP L 247 " --> pdb=" O TRP L 289 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA L 253 " --> pdb=" O TRP L 316 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP L 316 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU L 313 " --> pdb=" O GLU L 308 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 232 through 234 removed outlier: 3.877A pdb=" N GLU K 234 " --> pdb=" O CYS L 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS L 217 " --> pdb=" O GLU K 234 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG L 218 " --> pdb=" O ARG L 242 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 262 through 264 removed outlier: 4.146A pdb=" N PHE L 81 " --> pdb=" O ILE K 240 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AF1, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AF2, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AF3, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AF4, first strand: chain 'I' and resid 172 through 173 removed outlier: 3.907A pdb=" N GLY I 172 " --> pdb=" O LYS I 180 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.005A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.005A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA L 103 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU L 109 " --> pdb=" O PRO L 13 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU L 11 " --> pdb=" O LEU L 111 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 113 " --> pdb=" O LEU L 9 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU L 9 " --> pdb=" O VAL L 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 108 through 109 removed outlier: 3.530A pdb=" N ALA M 108 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.184A pdb=" N ALA M 157 " --> pdb=" O ARG M 218 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.890A pdb=" N ALA M 253 " --> pdb=" O MET M 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 44 through 47 Processing sheet with id=AG2, first strand: chain 'M' and resid 266 through 268 Processing sheet with id=AG3, first strand: chain 'N' and resid 108 through 109 removed outlier: 3.551A pdb=" N ALA N 108 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AG5, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AG6, first strand: chain 'N' and resid 44 through 50 Processing sheet with id=AG7, first strand: chain 'N' and resid 266 through 268 Processing sheet with id=AG8, first strand: chain 'N' and resid 287 through 288 removed outlier: 3.661A pdb=" N LYS N 293 " --> pdb=" O VAL N 288 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 108 through 109 Processing sheet with id=AH1, first strand: chain 'O' and resid 19 through 20 removed outlier: 4.721A pdb=" N LEU O 210 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL O 158 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP O 177 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL O 160 " --> pdb=" O ARG O 175 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG O 175 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE O 162 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR O 173 " --> pdb=" O ILE O 162 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS O 164 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AH3, first strand: chain 'O' and resid 44 through 50 removed outlier: 7.767A pdb=" N SER O 243 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR O 78 " --> pdb=" O SER O 243 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 287 through 288 removed outlier: 3.545A pdb=" N LYS O 293 " --> pdb=" O VAL O 288 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 108 through 109 Processing sheet with id=AH6, first strand: chain 'P' and resid 19 through 20 removed outlier: 4.700A pdb=" N LEU P 210 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL P 158 " --> pdb=" O ASP P 177 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP P 177 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL P 160 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG P 175 " --> pdb=" O VAL P 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE P 162 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR P 173 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS P 164 " --> pdb=" O ALA P 171 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 19 through 20 Processing sheet with id=AH8, first strand: chain 'P' and resid 44 through 51 removed outlier: 7.464A pdb=" N SER P 243 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR P 78 " --> pdb=" O SER P 243 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P' and resid 266 through 268 Processing sheet with id=AI1, first strand: chain 'P' and resid 287 through 288 Processing sheet with id=AI2, first strand: chain 'Q' and resid 108 through 109 Processing sheet with id=AI3, first strand: chain 'Q' and resid 19 through 20 removed outlier: 4.497A pdb=" N LEU Q 210 " --> pdb=" O ILE Q 165 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL Q 158 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP Q 177 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL Q 160 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG Q 175 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE Q 162 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR Q 173 " --> pdb=" O ILE Q 162 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS Q 164 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AI5, first strand: chain 'Q' and resid 44 through 51 removed outlier: 4.037A pdb=" N ASN Q 75 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER Q 243 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR Q 78 " --> pdb=" O SER Q 243 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 266 through 268 Processing sheet with id=AI7, first strand: chain 'Q' and resid 287 through 288 removed outlier: 3.559A pdb=" N LYS Q 293 " --> pdb=" O VAL Q 288 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 108 through 109 Processing sheet with id=AI9, first strand: chain 'R' and resid 19 through 20 removed outlier: 4.461A pdb=" N LEU R 210 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL R 158 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP R 177 " --> pdb=" O VAL R 158 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL R 160 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG R 175 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE R 162 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR R 173 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS R 164 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ2, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.256A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.256A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N HIS V 26 " --> pdb=" O THR V 41 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR V 41 " --> pdb=" O HIS V 26 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP V 28 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE V 39 " --> pdb=" O TRP V 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU V 30 " --> pdb=" O MET V 37 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 266 through 268 Processing sheet with id=AJ5, first strand: chain 'R' and resid 287 through 288 removed outlier: 3.748A pdb=" N VAL R 288 " --> pdb=" O LYS R 293 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS R 293 " --> pdb=" O VAL R 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ7, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ8, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AJ9, first strand: chain 'S' and resid 100 through 102 removed outlier: 3.590A pdb=" N PHE S 155 " --> pdb=" O LEU S 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU S 157 " --> pdb=" O VAL S 144 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'S' and resid 172 through 173 removed outlier: 3.586A pdb=" N GLY S 172 " --> pdb=" O LYS S 180 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'U' and resid 85 through 91 removed outlier: 7.747A pdb=" N VAL U 85 " --> pdb=" O ASN U 79 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN U 79 " --> pdb=" O VAL U 85 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR U 109 " --> pdb=" O VAL U 123 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'V' and resid 85 through 91 removed outlier: 7.748A pdb=" N VAL V 85 " --> pdb=" O ASN V 79 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASN V 79 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR V 109 " --> pdb=" O VAL V 123 " (cutoff:3.500A) 2128 hydrogen bonds defined for protein. 5805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 17.55 Time building geometry restraints manager: 20.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9668 1.33 - 1.45: 12056 1.45 - 1.57: 26547 1.57 - 1.69: 238 1.69 - 1.81: 71 Bond restraints: 48580 Sorted by residual: bond pdb=" C ARG I 73 " pdb=" N PRO I 74 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 8.93e+00 bond pdb=" C ARG S 73 " pdb=" N PRO S 74 " ideal model delta sigma weight residual 1.334 1.357 -0.023 8.40e-03 1.42e+04 7.47e+00 bond pdb=" CB ILE R 199 " pdb=" CG2 ILE R 199 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.76e+00 bond pdb=" CG1 ILE R 199 " pdb=" CD1 ILE R 199 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.88e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.54e+00 ... (remaining 48575 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.78: 2047 106.78 - 113.78: 26238 113.78 - 120.79: 21493 120.79 - 127.80: 15946 127.80 - 134.81: 657 Bond angle restraints: 66381 Sorted by residual: angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 110.05 102.48 7.57 1.09e+00 8.42e-01 4.82e+01 angle pdb=" N LEU B 181 " pdb=" CA LEU B 181 " pdb=" C LEU B 181 " ideal model delta sigma weight residual 109.81 121.43 -11.62 2.21e+00 2.05e-01 2.76e+01 angle pdb=" C ALA V 205 " pdb=" N ASN V 206 " pdb=" CA ASN V 206 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ALA U 205 " pdb=" N ASN U 206 " pdb=" CA ASN U 206 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C PHE S 15 " pdb=" N PRO S 16 " pdb=" CA PRO S 16 " ideal model delta sigma weight residual 119.66 123.03 -3.37 7.20e-01 1.93e+00 2.19e+01 ... (remaining 66376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 27324 35.04 - 70.08: 907 70.08 - 105.12: 100 105.12 - 140.16: 2 140.16 - 175.20: 12 Dihedral angle restraints: 28345 sinusoidal: 11704 harmonic: 16641 Sorted by residual: dihedral pdb=" O4' U J 39 " pdb=" C1' U J 39 " pdb=" N1 U J 39 " pdb=" C2 U J 39 " ideal model delta sinusoidal sigma weight residual 200.00 46.69 153.31 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' C J 37 " pdb=" C1' C J 37 " pdb=" N1 C J 37 " pdb=" C2 C J 37 " ideal model delta sinusoidal sigma weight residual 200.00 47.81 152.19 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" O4' U T 33 " pdb=" C1' U T 33 " pdb=" N1 U T 33 " pdb=" C2 U T 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.98 147.02 1 1.50e+01 4.44e-03 7.85e+01 ... (remaining 28342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 6195 0.070 - 0.139: 898 0.139 - 0.209: 85 0.209 - 0.278: 16 0.278 - 0.348: 3 Chirality restraints: 7197 Sorted by residual: chirality pdb=" CB ILE S 40 " pdb=" CA ILE S 40 " pdb=" CG1 ILE S 40 " pdb=" CG2 ILE S 40 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE F 232 " pdb=" CA ILE F 232 " pdb=" CG1 ILE F 232 " pdb=" CG2 ILE F 232 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA LEU B 181 " pdb=" N LEU B 181 " pdb=" C LEU B 181 " pdb=" CB LEU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 7194 not shown) Planarity restraints: 8509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 263 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 264 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 297 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO E 298 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 263 " -0.039 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO L 264 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO L 264 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 264 " -0.032 5.00e-02 4.00e+02 ... (remaining 8506 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 214 2.45 - 3.06: 28040 3.06 - 3.68: 73331 3.68 - 4.29: 108563 4.29 - 4.90: 177122 Nonbonded interactions: 387270 Sorted by model distance: nonbonded pdb=" CD2 LEU B 181 " pdb=" CD PRO B 182 " model vdw 1.839 3.860 nonbonded pdb=" O ASN N 75 " pdb=" OD1 ASN N 75 " model vdw 2.004 3.040 nonbonded pdb=" O ASP U 53 " pdb=" OD1 ASP U 53 " model vdw 2.063 3.040 nonbonded pdb=" O2' G J 40 " pdb=" C5' G J 41 " model vdw 2.103 3.440 nonbonded pdb=" CG PRO S 16 " pdb=" O2' G T 41 " model vdw 2.180 3.440 ... (remaining 387265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 103 or (resid 104 through 167 and (name N or na \ me CA or name C or name O )) or resid 168 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 through 202 or (resid \ 203 through 205 and (name N or name CA or name C or name O or name CB )) or resi \ d 206 through 223 or (resid 224 and (name N or name CA or name C or name O or na \ me CB )) or resid 225 through 227 or (resid 228 and (name N or name CA or name C \ or name O or name CB )) or resid 229 through 434)) selection = (chain 'K' and (resid 11 through 197 or (resid 198 and (name N or name CA or nam \ e C or name O or name CB )) or resid 199 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 or (resid 207 and (name \ N or name CA or name C or name O or name CB )) or resid 208 through 209 or (res \ id 210 and (name N or name CA or name C or name O or name CB )) or resid 211 thr \ ough 218 or (resid 219 through 222 and (name N or name CA or name C or name O or \ name CB )) or resid 223 through 226 or (resid 227 through 228 and (name N or na \ me CA or name C or name O or name CB )) or resid 229 through 257 or (resid 258 t \ hrough 259 and (name N or name CA or name C or name O or name CB )) or resid 260 \ through 265 or (resid 266 through 269 and (name N or name CA or name C or name \ O )) or resid 270 or resid 278 through 434)) } ncs_group { reference = (chain 'B' and (resid 3 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 75 or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB )) or resid 78 through 149 \ or (resid 150 through 151 and (name N or name CA or name C or name O or name CB \ )) or resid 152 through 166 or (resid 167 and (name N or name CA or name C or na \ me O or name CB )) or resid 168 through 188 or (resid 189 through 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 239 or (resi \ d 240 and (name N or name CA or name C or name O or name CB )) or resid 241 thro \ ugh 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) o \ r resid 287 through 322)) selection = (chain 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 51 or (resid 52 and (name N or na \ me CA or name C or name O or name CB )) or resid 53 through 62 or (resid 63 and \ (name N or name CA or name C or name O or name CB )) or resid 64 through 66 or ( \ resid 67 through 68 and (name N or name CA or name C or name O or name CB )) or \ resid 69 through 76 or (resid 77 and (name N or name CA or name C or name O or n \ ame CB )) or resid 78 through 93 or (resid 94 through 96 and (name N or name CA \ or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (nam \ e N or name CA or name C or name O or name CB )) or resid 109 through 112 or (re \ sid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 th \ rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 through 127 or (resid 128 and (name N or name CA or name C or name \ O or name CB )) or resid 129 through 146 or (resid 147 and (name N or name CA o \ r name C or name O or name CB )) or resid 148 through 157 or (resid 158 and (nam \ e N or name CA or name C or name O or name CB )) or resid 159 through 160 or (re \ sid 161 through 162 and (name N or name CA or name C or name O or name CB )) or \ resid 163 through 168 or (resid 169 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 or (resid 172 through 173 and (name N or n \ ame CA or name C or name O or name CB )) or resid 174 or (resid 175 and (name N \ or name CA or name C or name O or name CB )) or resid 176 through 177 or (resid \ 178 and (name N or name CA or name C or name O or name CB )) or resid 179 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 197 or (resid 198 and (name N or name CA or name C or name O o \ r name CB )) or resid 199 through 209 or (resid 210 and (name N or name CA or na \ me C or name O or name CB )) or resid 211 through 213 or (resid 214 and (name N \ or name CA or name C or name O or name CB )) or resid 215 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 223 or (resid 239 through 240 and (name N or name CA or name C or name O or na \ me CB )) or resid 241 through 265 or (resid 266 and (name N or name CA or name C \ or name O or name CB )) or resid 267 through 276 or (resid 277 and (name N or n \ ame CA or name C or name O or name CB )) or resid 278 through 281 or (resid 282 \ and (name N or name CA or name C or name O or name CB )) or resid 283 through 28 \ 9 or (resid 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 300 or (resid 301 and (name N or name CA or name C or name O or na \ me CB )) or resid 302 through 304 or (resid 305 and (name N or name CA or name C \ or name O or name CB )) or resid 306 through 313 or (resid 314 and (name N or n \ ame CA or name C or name O or name CB )) or resid 315 through 319 or (resid 320 \ and (name N or name CA or name C or name O or name CB )) or resid 321 through 32 \ 2)) } ncs_group { reference = (chain 'C' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 48 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 79 or (re \ sid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or \ resid 99 through 108 or (resid 109 through 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 through 113 or (resid 114 through 115 and ( \ name N or name CA or name C or name O or name CB )) or resid 116 or (resid 117 t \ hrough 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ through 132 or (resid 133 and (name N or name CA or name C or name O or name CB \ )) or resid 134 through 149 or (resid 150 and (name N or name CA or name C or n \ ame O or name CB )) or resid 151 through 161 or (resid 162 and (name N or name C \ A or name C or name O or name CB )) or resid 163 or (resid 164 and (name N or na \ me CA or name C or name O or name CB )) or resid 165 through 207 or (resid 208 a \ nd (name N or name CA or name C or name O or name CB )) or resid 209 through 217 \ or (resid 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 273 or (resid 274 through 275 and (name N or name C \ A or name C or name O or name CB )) or resid 276 or (resid 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 through 282 or (resid 283 a \ nd (name N or name CA or name C or name O or name CB )) or resid 284 or (resid 2 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 286 through \ 306 or (resid 307 and (name N or name CA or name C or name O or name CB )) or r \ esid 308 through 320 or (resid 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 326 or (resid 327 through 328 and (name N or na \ me CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name N o \ r name CA or name C or name O or 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(name N or name CA or name C or name O or name CB )) \ or resid 272 through 273 or (resid 274 through 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or \ name C or name O or name CB )) or resid 278 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 or (resid 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 290 or \ (resid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 \ through 295 or (resid 296 through 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 301 or (resid 302 through 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 through 306 or (res \ id 307 and (name N or name CA or name C or name O or name CB )) or resid 308 thr \ ough 313 or (resid 314 and (name N or name CA or name C or name O or name CB )) \ or resid 315 through 320 or (resid 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 323 or (resid 324 and (name N or name CA or \ name C or name O or name CB )) or resid 325 through 326 or (resid 327 through 3 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 329 or (res \ id 330 and (name N or name CA or name C or name O or name CB )) or resid 331 thr \ ough 338)) selection = (chain 'N' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or nam \ e CA or name C or name O or name CB )) or resid 286 through 290 or (resid 291 an \ d (name N or name CA or name C or name O or name CB )) or resid 292 through 295 \ or (resid 296 through 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 313 or ( \ resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 320 or (resid 321 and (name N or name CA or name C or name O or name CB \ )) or resid 322 through 323 or (resid 324 and (name N or name CA or name C or na \ me O or name CB )) or resid 325 through 326 or (resid 327 through 328 and (name \ N or name CA or name C or name O or name CB )) or resid 329 or (resid 330 and (n \ ame N or name CA or name C or name O or name CB )) or resid 331 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or nam \ e CA or name C or name O or name CB )) or resid 286 through 290 or (resid 291 an \ d (name N or name CA or name C or name O or name CB )) or resid 292 through 295 \ or (resid 296 through 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 313 or ( \ resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 320 or (resid 321 and (name N or name CA or name C or name O or name CB \ )) or resid 322 through 323 or (resid 324 and (name N or name CA or name C or na \ me O or name CB )) or resid 325 through 326 or (resid 327 through 328 and (name \ N or name CA or name C or name O or name CB )) or resid 329 or (resid 330 and (n \ ame N or name CA or name C or name O or name CB )) or resid 331 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 284 or (resid 285 and (name N or name CA \ or name C or name O or name CB )) or resid 286 through 290 or (resid 291 and (n \ ame N or name CA or name C or name O or name CB )) or resid 292 through 295 or ( \ resid 296 through 297 and (name N or name CA or name C or name O or name CB )) o \ r resid 298 or (resid 299 and (name N or name CA or name C or name O or name CB \ )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA or \ name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (name \ N or name CA or name C or name O or name CB )) or resid 308 through 313 or (resi \ d 314 and (name N or name CA or name C or name O or name CB )) or resid 315 thro \ ugh 320 or (resid 321 and (name N or name CA or name C or name O or name CB )) o \ r resid 322 through 323 or (resid 324 and (name N or name CA or name C or name O \ or name CB )) or resid 325 through 326 or (resid 327 through 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name \ N or name CA or name C or name O or name CB )) or resid 331 through 337 or (resi \ d 338 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or resid 244 through 245 or (resid 246 and (n \ ame N or name CA or name C or name O or name CB )) or resid 247 through 249 or ( \ resid 250 and (name N or name CA or name C or name O or name CB )) or resid 251 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 276 or (resid 277 and (name N or name CA or name C or na \ me O or name CB )) or resid 278 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 or (resid 285 and (name N or nam \ e CA or name C or name O or name CB )) or resid 286 through 290 or (resid 291 an \ d (name N or name CA or name C or name O or name CB )) or resid 292 through 295 \ or (resid 296 through 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or name \ CB )) or resid 300 through 301 or (resid 302 through 303 and (name N or name CA \ or name C or name O or name CB )) or resid 304 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 313 or ( \ resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 323 or (resid 324 and (name N or name CA or name C or name O or name CB \ )) or resid 325 through 326 or (resid 327 through 328 and (name N or name CA or \ name C or name O or name CB )) or resid 329 or (resid 330 and (name N or name CA \ or name C or name O or name CB )) or resid 331 through 337 or (resid 338 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 113 or (r \ esid 114 through 115 and (name N or name CA or name C or name O or name CB )) or \ resid 116 or (resid 117 through 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 through 130 or (resid 131 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 1 \ 39 or (resid 140 and (name N or name CA or name C or name O or name CB )) or res \ id 141 through 149 or (resid 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 155 or (resid 156 through 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 or (resid 159 and (name N or \ name CA or name C or name O or name CB )) or resid 160 or (resid 161 through 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throu \ gh 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or \ resid 170 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 207 or (resid 208 and (name N or name CA or n \ ame C or name O or name CB )) or resid 209 or (resid 210 and (name N or name CA \ or name C or name O or name CB )) or resid 211 through 217 or (resid 218 and (na \ me N or name CA or name C or name O or name CB )) or resid 219 through 228 or (r \ esid 229 and (name N or name CA or name C or name O or name CB )) or resid 230 o \ r resid 244 through 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 249 or (resid 250 and (name N or name CA or \ name C or name O or name CB )) or resid 251 through 270 or (resid 271 and (name \ N or name CA or name C or name O or name CB )) or resid 272 through 276 or (resi \ d 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 282 or (resid 283 and (name N or name CA or name C or name O or name CB )) o \ r resid 284 or (resid 285 and (name N or name CA or name C or name O or name CB \ )) or resid 286 through 290 or (resid 291 and (name N or name CA or name C or na \ me O or name CB )) or resid 292 through 295 or (resid 296 through 297 and (name \ N or name CA or name C or name O or name CB )) or resid 298 or (resid 299 and (n \ ame N or name CA or name C or name O or name CB )) or resid 300 through 301 or ( \ resid 302 through 303 and (name N or name CA or name C or name O or name CB )) o \ r resid 304 through 306 or (resid 307 and (name N or name CA or name C or name O \ or name CB )) or resid 308 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 320 or (resid 321 and (name \ N or name CA or name C or name O or name CB )) or resid 322 through 323 or (resi \ d 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thro \ ugh 329 or (resid 330 and (name N or name CA or name C or name O or name CB )) o \ r resid 331 through 337 or (resid 338 and (name N or name CA or name C or name O \ or name CB )))) } ncs_group { reference = (chain 'I' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 142 or (resid 143 and (name N or na \ me CA or name C or name O or name CB )) or resid 144 through 152 or (resid 153 a \ nd (name N or name CA or name C or name O or name CB )) or resid 154 through 174 \ or resid 176 through 177 or (resid 178 and (name N or name CA or name C or name \ O or name CB )) or resid 179 through 187)) selection = (chain 'S' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.030 Extract box with map and model: 9.730 Check model and map are aligned: 0.770 Set scattering table: 0.460 Process input model: 129.060 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 48580 Z= 0.360 Angle : 0.783 12.819 66381 Z= 0.451 Chirality : 0.051 0.348 7197 Planarity : 0.006 0.064 8509 Dihedral : 17.109 175.197 18021 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 0.40 % Allowed : 10.89 % Favored : 88.71 % 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: -3.08 (0.09), residues: 6146 helix: -2.32 (0.08), residues: 1913 sheet: 0.21 (0.15), residues: 1032 loop : -2.72 (0.09), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 263 HIS 0.014 0.001 HIS S 3 PHE 0.026 0.002 PHE L 152 TYR 0.022 0.002 TYR P 271 ARG 0.009 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 475 time to evaluate : 5.386 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: A 232 PHE cc_start: 0.6678 (p90) cc_final: 0.6466 (p90) REVERT: A 249 GLN cc_start: 0.6553 (pm20) cc_final: 0.6158 (tp-100) REVERT: B 306 HIS cc_start: 0.5762 (p90) cc_final: 0.5264 (p90) REVERT: C 127 ASN cc_start: 0.7209 (m110) cc_final: 0.6792 (m110) REVERT: C 138 TYR cc_start: 0.8484 (m-10) cc_final: 0.8184 (m-10) REVERT: C 167 GLN cc_start: 0.7620 (tp40) cc_final: 0.7291 (tm-30) REVERT: C 295 TYR cc_start: 0.7791 (m-80) cc_final: 0.7579 (m-80) REVERT: K 271 HIS cc_start: 0.7909 (m-70) cc_final: 0.7503 (m-70) REVERT: I 1 MET cc_start: -0.0715 (mtm) cc_final: -0.1642 (ppp) REVERT: I 21 MET cc_start: 0.4033 (ptt) cc_final: 0.3058 (ttt) REVERT: L 321 PHE cc_start: 0.6799 (p90) cc_final: 0.6204 (t80) REVERT: M 30 TRP cc_start: 0.7033 (t-100) cc_final: 0.6177 (t-100) outliers start: 17 outliers final: 10 residues processed: 490 average time/residue: 1.7372 time to fit residues: 1037.5237 Evaluate side-chains 279 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain N residue 250 ARG 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 U residue 46 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 0.3980 chunk 471 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 161 optimal weight: 0.2980 chunk 318 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 487 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 296 optimal weight: 50.0000 chunk 362 optimal weight: 0.7980 chunk 564 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS B 129 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 240 GLN C 77 GLN C 127 ASN C 151 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 208 HIS D 329 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN E 223 GLN E 262 ASN E 300 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN H 127 ASN H 129 GLN H 223 GLN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 HIS L 133 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN L 196 HIS M 120 GLN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 GLN N 127 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 223 GLN ** P 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 GLN Q 241 GLN Q 291 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 GLN S 82 HIS S 84 GLN U 2 ASN V 2 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48580 Z= 0.172 Angle : 0.547 13.361 66381 Z= 0.290 Chirality : 0.041 0.317 7197 Planarity : 0.004 0.095 8509 Dihedral : 15.368 178.687 8612 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.87 % Allowed : 15.74 % Favored : 82.39 % 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: -1.58 (0.10), residues: 6146 helix: -0.21 (0.11), residues: 1930 sheet: 0.42 (0.15), residues: 1078 loop : -2.20 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 147 HIS 0.010 0.001 HIS B 196 PHE 0.016 0.001 PHE B 321 TYR 0.015 0.001 TYR C 325 ARG 0.009 0.000 ARG H 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 294 time to evaluate : 5.485 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: A 232 PHE cc_start: 0.6820 (p90) cc_final: 0.6285 (p90) REVERT: A 238 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 249 GLN cc_start: 0.6428 (pm20) cc_final: 0.6138 (tp-100) REVERT: B 240 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: B 278 ARG cc_start: 0.4995 (OUTLIER) cc_final: 0.4358 (mtp85) REVERT: B 306 HIS cc_start: 0.5716 (p90) cc_final: 0.5252 (p90) REVERT: C 127 ASN cc_start: 0.7499 (m-40) cc_final: 0.7017 (m110) REVERT: C 138 TYR cc_start: 0.8490 (m-10) cc_final: 0.8175 (m-10) REVERT: C 149 TRP cc_start: 0.7845 (m100) cc_final: 0.7367 (m-10) REVERT: C 259 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7678 (mmtt) REVERT: K 271 HIS cc_start: 0.7871 (m-70) cc_final: 0.7570 (m-70) REVERT: I 1 MET cc_start: -0.0763 (mtm) cc_final: -0.1696 (ppp) REVERT: I 21 MET cc_start: 0.3739 (ptt) cc_final: 0.2712 (ttm) REVERT: L 320 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7278 (ptt-90) REVERT: L 321 PHE cc_start: 0.6956 (p90) cc_final: 0.6238 (t80) REVERT: M 30 TRP cc_start: 0.7045 (t-100) cc_final: 0.6232 (t-100) REVERT: V 46 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8431 (m-80) outliers start: 79 outliers final: 24 residues processed: 357 average time/residue: 1.5216 time to fit residues: 681.0850 Evaluate side-chains 278 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 249 time to evaluate : 5.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 278 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain K residue 230 HIS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 320 ARG Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 120 GLN Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 470 optimal weight: 4.9990 chunk 384 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 565 optimal weight: 0.9990 chunk 611 optimal weight: 5.9990 chunk 503 optimal weight: 5.9990 chunk 561 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 453 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 196 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN H 300 GLN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 HIS Q 329 ASN R 77 GLN R 164 HIS U 2 ASN U 154 HIS V 2 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 48580 Z= 0.252 Angle : 0.551 10.844 66381 Z= 0.290 Chirality : 0.041 0.241 7197 Planarity : 0.004 0.066 8509 Dihedral : 15.276 179.496 8602 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.53 % Allowed : 16.66 % Favored : 80.80 % 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: -0.88 (0.10), residues: 6146 helix: 0.76 (0.11), residues: 1933 sheet: 0.58 (0.15), residues: 1067 loop : -1.96 (0.10), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 263 HIS 0.013 0.001 HIS B 196 PHE 0.036 0.001 PHE C 304 TYR 0.020 0.002 TYR H 325 ARG 0.005 0.000 ARG R 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 256 time to evaluate : 5.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 232 PHE cc_start: 0.6846 (p90) cc_final: 0.6251 (p90) REVERT: A 238 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 200 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7767 (pp) REVERT: B 306 HIS cc_start: 0.5736 (p90) cc_final: 0.5361 (p90) REVERT: C 127 ASN cc_start: 0.7615 (m-40) cc_final: 0.7117 (m110) REVERT: C 138 TYR cc_start: 0.8475 (m-10) cc_final: 0.8090 (m-10) REVERT: C 149 TRP cc_start: 0.7866 (m100) cc_final: 0.7390 (m-10) REVERT: C 259 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7642 (mmtt) REVERT: E 250 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7473 (mtp180) REVERT: F 285 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: G 231 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8625 (tp) REVERT: K 271 HIS cc_start: 0.7912 (m-70) cc_final: 0.7648 (m-70) REVERT: I 1 MET cc_start: -0.0762 (mtm) cc_final: -0.1724 (ppp) REVERT: I 21 MET cc_start: 0.4161 (ptt) cc_final: 0.3096 (ttm) REVERT: L 320 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7228 (ptt-90) REVERT: L 321 PHE cc_start: 0.6878 (p90) cc_final: 0.6221 (t80) REVERT: M 30 TRP cc_start: 0.7113 (t-100) cc_final: 0.6427 (t-100) REVERT: N 218 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7607 (ttt90) REVERT: N 283 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: V 46 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8407 (m-80) outliers start: 107 outliers final: 45 residues processed: 347 average time/residue: 1.4891 time to fit residues: 653.0521 Evaluate side-chains 290 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 235 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 167 GLN 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 110 ASN Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain L residue 320 ARG Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 120 GLN Chi-restraints excluded: chain P residue 250 ARG Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 105 ASP Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 2.9990 chunk 425 optimal weight: 0.1980 chunk 293 optimal weight: 0.0040 chunk 62 optimal weight: 9.9990 chunk 270 optimal weight: 0.5980 chunk 379 optimal weight: 6.9990 chunk 567 optimal weight: 3.9990 chunk 601 optimal weight: 0.3980 chunk 296 optimal weight: 50.0000 chunk 538 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN I 108 ASN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 HIS O 120 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN V 2 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 48580 Z= 0.130 Angle : 0.494 9.904 66381 Z= 0.258 Chirality : 0.039 0.187 7197 Planarity : 0.003 0.076 8509 Dihedral : 15.114 179.158 8600 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.08 % Allowed : 17.51 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 6146 helix: 1.33 (0.12), residues: 1922 sheet: 0.68 (0.15), residues: 1103 loop : -1.80 (0.10), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 174 HIS 0.006 0.001 HIS S 3 PHE 0.023 0.001 PHE C 304 TYR 0.024 0.001 TYR H 325 ARG 0.007 0.000 ARG G 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 296 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 PHE cc_start: 0.6839 (p90) cc_final: 0.6235 (p90) REVERT: A 238 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 241 GLN cc_start: 0.5775 (mp10) cc_final: 0.5535 (mp10) REVERT: B 200 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7923 (pp) REVERT: B 306 HIS cc_start: 0.5781 (p90) cc_final: 0.5333 (p90) REVERT: C 127 ASN cc_start: 0.7601 (m-40) cc_final: 0.7121 (m110) REVERT: C 138 TYR cc_start: 0.8512 (m-10) cc_final: 0.8132 (m-10) REVERT: C 149 TRP cc_start: 0.7807 (m100) cc_final: 0.7435 (m100) REVERT: D 46 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6676 (tp30) REVERT: D 241 GLN cc_start: 0.8262 (mp10) cc_final: 0.7845 (mp10) REVERT: K 261 GLU cc_start: 0.8366 (tt0) cc_final: 0.8095 (tm-30) REVERT: K 271 HIS cc_start: 0.7830 (m-70) cc_final: 0.7559 (m-70) REVERT: I 1 MET cc_start: -0.0103 (mtm) cc_final: -0.2215 (ppp) REVERT: I 21 MET cc_start: 0.4221 (ptt) cc_final: 0.3144 (ttm) REVERT: L 198 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: L 210 LEU cc_start: 0.8227 (tm) cc_final: 0.7803 (tm) REVERT: L 320 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7188 (ptt-90) REVERT: L 321 PHE cc_start: 0.6879 (p90) cc_final: 0.6220 (t80) REVERT: M 30 TRP cc_start: 0.6979 (t-100) cc_final: 0.6156 (t-100) REVERT: S 1 MET cc_start: 0.2451 (ptp) cc_final: 0.1897 (ptt) REVERT: S 67 LEU cc_start: 0.1770 (OUTLIER) cc_final: 0.1101 (mp) REVERT: U 46 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7651 (t80) REVERT: V 46 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: V 209 LYS cc_start: 0.9090 (mttm) cc_final: 0.8701 (mmmt) outliers start: 88 outliers final: 37 residues processed: 373 average time/residue: 1.4896 time to fit residues: 702.1828 Evaluate side-chains 296 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 5.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 198 GLU Chi-restraints excluded: chain L residue 320 ARG Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 120 GLN Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 67 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 105 ASP Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 447 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 513 optimal weight: 0.0870 chunk 415 optimal weight: 3.9990 chunk 0 optimal weight: 70.0000 chunk 307 optimal weight: 20.0000 chunk 539 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 120 GLN G 72 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 208 HIS ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN R 120 GLN U 2 ASN V 2 ASN V 154 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 48580 Z= 0.432 Angle : 0.634 10.657 66381 Z= 0.332 Chirality : 0.044 0.209 7197 Planarity : 0.005 0.079 8509 Dihedral : 15.255 176.099 8600 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.89 % Allowed : 18.18 % Favored : 78.93 % 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: -0.44 (0.11), residues: 6146 helix: 1.33 (0.12), residues: 1914 sheet: 0.67 (0.15), residues: 1061 loop : -1.75 (0.11), residues: 3171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 247 HIS 0.009 0.002 HIS G 256 PHE 0.019 0.002 PHE U 212 TYR 0.026 0.002 TYR E 271 ARG 0.006 0.001 ARG I 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 238 time to evaluate : 5.583 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: A 232 PHE cc_start: 0.6850 (p90) cc_final: 0.6178 (p90) REVERT: A 238 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 261 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6053 (tp30) REVERT: B 137 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5947 (pmm) REVERT: B 200 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7879 (pp) REVERT: B 258 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4014 (mt) REVERT: B 306 HIS cc_start: 0.5847 (p90) cc_final: 0.5570 (p90) REVERT: C 127 ASN cc_start: 0.7770 (m-40) cc_final: 0.7260 (m110) REVERT: C 138 TYR cc_start: 0.8494 (m-10) cc_final: 0.8128 (m-10) REVERT: C 149 TRP cc_start: 0.7858 (m100) cc_final: 0.7382 (m-10) REVERT: E 250 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7556 (mtp85) REVERT: G 172 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6851 (ttt180) REVERT: H 295 TYR cc_start: 0.6853 (m-80) cc_final: 0.6636 (m-10) REVERT: I 1 MET cc_start: -0.0752 (mtm) cc_final: -0.3085 (ppp) REVERT: I 21 MET cc_start: 0.3919 (ptt) cc_final: 0.2674 (ttm) REVERT: L 321 PHE cc_start: 0.6871 (p90) cc_final: 0.6239 (t80) REVERT: M 30 TRP cc_start: 0.7120 (t-100) cc_final: 0.6255 (t-100) REVERT: M 271 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6471 (p90) REVERT: N 218 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7669 (ttt90) REVERT: N 283 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: O 285 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: S 29 HIS cc_start: 0.3388 (OUTLIER) cc_final: 0.2555 (m170) REVERT: V 46 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8554 (m-80) outliers start: 122 outliers final: 53 residues processed: 337 average time/residue: 1.5689 time to fit residues: 669.7806 Evaluate side-chains 285 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 219 time to evaluate : 5.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 160 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 243 SER Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain G residue 172 ARG Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 140 HIS Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 172 ARG Chi-restraints excluded: chain P residue 250 ARG Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 112 LEU 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 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 0.6980 chunk 541 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 601 optimal weight: 0.0060 chunk 499 optimal weight: 0.0870 chunk 278 optimal weight: 50.0000 chunk 50 optimal weight: 0.5980 chunk 199 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 overall best weight: 0.8776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 82 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 HIS ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 HIS ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN U 2 ASN V 2 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 48580 Z= 0.159 Angle : 0.517 9.718 66381 Z= 0.271 Chirality : 0.040 0.174 7197 Planarity : 0.003 0.057 8509 Dihedral : 15.137 177.511 8600 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.20 % Allowed : 19.15 % Favored : 78.65 % 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: -0.15 (0.11), residues: 6146 helix: 1.63 (0.12), residues: 1915 sheet: 0.83 (0.15), residues: 1059 loop : -1.61 (0.11), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP H 311 HIS 0.012 0.001 HIS A 203 PHE 0.016 0.001 PHE A 211 TYR 0.025 0.001 TYR H 325 ARG 0.008 0.000 ARG F 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 249 time to evaluate : 5.317 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: A 232 PHE cc_start: 0.6798 (p90) cc_final: 0.6167 (p90) REVERT: A 238 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 261 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5939 (tp30) REVERT: B 200 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7825 (pp) REVERT: B 243 ASP cc_start: 0.6916 (t70) cc_final: 0.6665 (t0) REVERT: B 258 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.3889 (mt) REVERT: B 306 HIS cc_start: 0.5826 (p90) cc_final: 0.5458 (p90) REVERT: C 127 ASN cc_start: 0.7670 (m-40) cc_final: 0.7174 (m110) REVERT: C 138 TYR cc_start: 0.8461 (m-10) cc_final: 0.8085 (m-10) REVERT: C 149 TRP cc_start: 0.7866 (m100) cc_final: 0.7499 (m-10) REVERT: F 285 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: I 1 MET cc_start: -0.0579 (mtm) cc_final: -0.2752 (ppp) REVERT: I 21 MET cc_start: 0.3947 (ptt) cc_final: 0.2756 (ttm) REVERT: L 198 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: L 210 LEU cc_start: 0.8361 (tm) cc_final: 0.7828 (tm) REVERT: L 321 PHE cc_start: 0.6888 (p90) cc_final: 0.6232 (t80) REVERT: M 30 TRP cc_start: 0.7099 (t-100) cc_final: 0.6167 (t-100) REVERT: N 218 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7610 (ttt90) REVERT: N 283 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: O 129 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: V 46 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8348 (m-80) outliers start: 93 outliers final: 45 residues processed: 329 average time/residue: 1.5034 time to fit residues: 625.8758 Evaluate side-chains 284 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 5.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 198 GLU Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 129 GLN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 105 ASP Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 439 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 506 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 chunk 599 optimal weight: 2.9990 chunk 375 optimal weight: 5.9990 chunk 365 optimal weight: 0.4980 chunk 276 optimal weight: 50.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN U 2 ASN V 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 48580 Z= 0.229 Angle : 0.529 10.060 66381 Z= 0.277 Chirality : 0.040 0.183 7197 Planarity : 0.004 0.054 8509 Dihedral : 15.096 177.538 8600 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.85 % Allowed : 20.19 % Favored : 77.96 % 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: 6146 helix: 1.70 (0.12), residues: 1915 sheet: 0.81 (0.15), residues: 1068 loop : -1.60 (0.11), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 263 HIS 0.024 0.001 HIS A 203 PHE 0.015 0.001 PHE L 184 TYR 0.026 0.001 TYR H 325 ARG 0.011 0.000 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 233 time to evaluate : 5.551 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: A 238 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 261 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5786 (tp30) REVERT: B 200 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7872 (pp) REVERT: B 258 LEU cc_start: 0.4898 (OUTLIER) cc_final: 0.3938 (mt) REVERT: B 306 HIS cc_start: 0.5760 (p90) cc_final: 0.5363 (p90) REVERT: C 127 ASN cc_start: 0.7695 (m-40) cc_final: 0.7196 (m110) REVERT: C 138 TYR cc_start: 0.8436 (m-10) cc_final: 0.8097 (m-10) REVERT: C 149 TRP cc_start: 0.7875 (m100) cc_final: 0.7626 (m100) REVERT: F 285 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: I 1 MET cc_start: -0.0497 (mtm) cc_final: -0.2994 (ppp) REVERT: I 21 MET cc_start: 0.4018 (ptt) cc_final: 0.2759 (ttm) REVERT: L 210 LEU cc_start: 0.8387 (tm) cc_final: 0.7857 (tm) REVERT: L 321 PHE cc_start: 0.6900 (p90) cc_final: 0.6208 (t80) REVERT: M 30 TRP cc_start: 0.7108 (t-100) cc_final: 0.6400 (t-100) REVERT: N 218 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7661 (ttt90) REVERT: N 283 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6891 (mm-30) REVERT: S 29 HIS cc_start: 0.3262 (OUTLIER) cc_final: 0.2429 (m170) REVERT: V 46 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8358 (m-80) outliers start: 78 outliers final: 46 residues processed: 299 average time/residue: 1.4723 time to fit residues: 558.7586 Evaluate side-chains 283 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 228 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 170 VAL 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 H residue 110 ASN Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain L residue 295 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 129 GLN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 250 ARG Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 105 ASP Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 381 optimal weight: 0.2980 chunk 408 optimal weight: 3.9990 chunk 296 optimal weight: 60.0000 chunk 55 optimal weight: 20.0000 chunk 471 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN H 127 ASN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN U 2 ASN V 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 48580 Z= 0.197 Angle : 0.522 10.028 66381 Z= 0.273 Chirality : 0.040 0.180 7197 Planarity : 0.004 0.052 8509 Dihedral : 15.063 178.987 8600 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.04 % Allowed : 20.33 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 6146 helix: 1.78 (0.12), residues: 1915 sheet: 0.92 (0.16), residues: 1056 loop : -1.57 (0.11), residues: 3175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 263 HIS 0.012 0.001 HIS A 203 PHE 0.017 0.001 PHE A 211 TYR 0.031 0.001 TYR H 325 ARG 0.012 0.000 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 239 time to evaluate : 5.560 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: A 232 PHE cc_start: 0.6741 (p90) cc_final: 0.6277 (p90) REVERT: A 238 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 200 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7861 (pp) REVERT: B 258 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.4220 (mt) REVERT: B 306 HIS cc_start: 0.5755 (p90) cc_final: 0.5357 (p90) REVERT: C 127 ASN cc_start: 0.7691 (m-40) cc_final: 0.7193 (m110) REVERT: C 149 TRP cc_start: 0.7862 (m100) cc_final: 0.7537 (m100) REVERT: F 285 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: I 1 MET cc_start: -0.0514 (mtm) cc_final: -0.3011 (ppp) REVERT: I 21 MET cc_start: 0.4110 (ptt) cc_final: 0.2838 (ttm) REVERT: I 117 MET cc_start: -0.0361 (tpt) cc_final: -0.0624 (tpt) REVERT: L 210 LEU cc_start: 0.8363 (tm) cc_final: 0.7858 (tm) REVERT: L 321 PHE cc_start: 0.6778 (p90) cc_final: 0.6146 (t80) REVERT: M 30 TRP cc_start: 0.7123 (t-100) cc_final: 0.6265 (t-100) REVERT: N 218 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7661 (ttt90) REVERT: N 283 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: O 129 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: S 29 HIS cc_start: 0.3285 (OUTLIER) cc_final: 0.2390 (m170) REVERT: U 37 MET cc_start: 0.8265 (mtp) cc_final: 0.8007 (mtm) REVERT: V 46 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8298 (m-80) outliers start: 86 outliers final: 48 residues processed: 310 average time/residue: 1.4109 time to fit residues: 559.8597 Evaluate side-chains 285 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 208 HIS 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 285 TYR Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 295 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 129 GLN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 283 GLU Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 0.9980 chunk 574 optimal weight: 5.9990 chunk 524 optimal weight: 4.9990 chunk 558 optimal weight: 40.0000 chunk 336 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 438 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 504 optimal weight: 0.8980 chunk 528 optimal weight: 3.9990 chunk 556 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN U 2 ASN V 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 48580 Z= 0.232 Angle : 0.537 10.070 66381 Z= 0.281 Chirality : 0.040 0.184 7197 Planarity : 0.004 0.058 8509 Dihedral : 15.035 179.765 8600 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.04 % Allowed : 20.28 % Favored : 77.68 % 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: -0.00 (0.11), residues: 6146 helix: 1.81 (0.12), residues: 1903 sheet: 0.83 (0.15), residues: 1085 loop : -1.53 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 263 HIS 0.014 0.001 HIS A 203 PHE 0.019 0.001 PHE A 211 TYR 0.032 0.001 TYR H 325 ARG 0.015 0.000 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 227 time to evaluate : 5.813 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: A 232 PHE cc_start: 0.6670 (p90) cc_final: 0.6098 (p90) REVERT: A 242 LYS cc_start: 0.6244 (mmmt) cc_final: 0.5772 (tppt) REVERT: B 200 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7851 (pp) REVERT: B 258 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4110 (mt) REVERT: B 306 HIS cc_start: 0.5721 (p90) cc_final: 0.5407 (p90) REVERT: C 127 ASN cc_start: 0.7712 (m-40) cc_final: 0.7213 (m110) REVERT: C 149 TRP cc_start: 0.7882 (m100) cc_final: 0.7567 (m-10) REVERT: C 259 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7634 (mmtt) REVERT: F 285 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: I 1 MET cc_start: -0.0402 (mtm) cc_final: -0.2873 (ppp) REVERT: I 21 MET cc_start: 0.4241 (ptt) cc_final: 0.2942 (ttm) REVERT: L 210 LEU cc_start: 0.8404 (tm) cc_final: 0.7936 (tm) REVERT: L 321 PHE cc_start: 0.6775 (p90) cc_final: 0.6142 (t80) REVERT: M 30 TRP cc_start: 0.7183 (t-100) cc_final: 0.6429 (t-100) REVERT: N 218 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7701 (ttt90) REVERT: N 283 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: S 29 HIS cc_start: 0.3300 (OUTLIER) cc_final: 0.2449 (m170) REVERT: V 46 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8338 (m-80) outliers start: 86 outliers final: 59 residues processed: 300 average time/residue: 1.4504 time to fit residues: 554.4901 Evaluate side-chains 285 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 218 time to evaluate : 5.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain L residue 295 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 129 GLN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 250 ARG Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 66 LYS Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 105 ASP Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 8.9990 chunk 590 optimal weight: 0.6980 chunk 360 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 chunk 410 optimal weight: 0.0770 chunk 619 optimal weight: 7.9990 chunk 570 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 381 optimal weight: 0.8980 chunk 302 optimal weight: 30.0000 overall best weight: 2.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 329 ASN U 2 ASN V 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 48580 Z= 0.279 Angle : 0.558 10.150 66381 Z= 0.293 Chirality : 0.041 0.248 7197 Planarity : 0.004 0.060 8509 Dihedral : 15.054 179.013 8600 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.80 % Allowed : 20.71 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 6146 helix: 1.77 (0.12), residues: 1902 sheet: 0.77 (0.15), residues: 1098 loop : -1.54 (0.11), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 263 HIS 0.019 0.001 HIS A 203 PHE 0.047 0.001 PHE C 304 TYR 0.032 0.002 TYR H 325 ARG 0.013 0.000 ARG G 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12292 Ramachandran restraints generated. 6146 Oldfield, 0 Emsley, 6146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 5.280 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: A 232 PHE cc_start: 0.6662 (p90) cc_final: 0.6108 (p90) REVERT: B 258 LEU cc_start: 0.5018 (OUTLIER) cc_final: 0.4137 (mt) REVERT: B 306 HIS cc_start: 0.5740 (p90) cc_final: 0.5423 (p90) REVERT: C 127 ASN cc_start: 0.7785 (m-40) cc_final: 0.7263 (m110) REVERT: C 149 TRP cc_start: 0.7914 (m100) cc_final: 0.7691 (m100) REVERT: C 259 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7783 (mmtt) REVERT: F 285 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: I 1 MET cc_start: -0.0387 (mtm) cc_final: -0.2961 (ppp) REVERT: I 21 MET cc_start: 0.4152 (ptt) cc_final: 0.2765 (ttm) REVERT: L 210 LEU cc_start: 0.8401 (tm) cc_final: 0.7948 (tm) REVERT: L 321 PHE cc_start: 0.6759 (p90) cc_final: 0.6133 (t80) REVERT: M 30 TRP cc_start: 0.7245 (t-100) cc_final: 0.6322 (t-100) REVERT: N 218 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7709 (ttt90) REVERT: N 283 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: S 29 HIS cc_start: 0.3371 (OUTLIER) cc_final: 0.2508 (m170) REVERT: V 46 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8361 (m-80) outliers start: 76 outliers final: 56 residues processed: 281 average time/residue: 1.4858 time to fit residues: 531.4773 Evaluate side-chains 273 residues out of total 5017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 5.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 239 TRP Chi-restraints excluded: chain L residue 295 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain N residue 283 GLU Chi-restraints excluded: chain O residue 129 GLN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 206 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 250 ARG Chi-restraints excluded: chain P residue 277 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 234 ASP Chi-restraints excluded: chain Q residue 283 GLU Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 105 ASP Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain V residue 46 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 1.9990 chunk 525 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 454 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 494 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 507 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 203 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** L 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 ASN Q 329 ASN ** R 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN V 2 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094376 restraints weight = 97798.877| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.95 r_work: 0.3072 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 48580 Z= 0.231 Angle : 0.546 11.898 66381 Z= 0.284 Chirality : 0.041 0.240 7197 Planarity : 0.004 0.059 8509 Dihedral : 15.034 178.797 8600 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.82 % Allowed : 20.85 % Favored : 77.33 % 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: -0.01 (0.11), residues: 6146 helix: 1.80 (0.12), residues: 1902 sheet: 0.84 (0.15), residues: 1088 loop : -1.54 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 263 HIS 0.019 0.001 HIS A 203 PHE 0.042 0.001 PHE C 304 TYR 0.035 0.001 TYR H 325 ARG 0.013 0.000 ARG G 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14087.85 seconds wall clock time: 250 minutes 47.49 seconds (15047.49 seconds total)