Starting phenix.real_space_refine on Fri Dec 27 16:50:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eln_31186/12_2024/7eln_31186.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eln_31186/12_2024/7eln_31186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eln_31186/12_2024/7eln_31186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eln_31186/12_2024/7eln_31186.map" model { file = "/net/cci-nas-00/data/ceres_data/7eln_31186/12_2024/7eln_31186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eln_31186/12_2024/7eln_31186.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 170 5.49 5 S 46 5.16 5 C 29935 2.51 5 N 9012 2.21 5 O 9743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48906 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2198 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2144 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2531 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2587 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 324} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2577 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2523 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2487 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 12, 'TRANS': 319} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2321 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2227 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "N" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2571 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2562 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2581 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2529 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1442 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1442 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1477 Chain: "U" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "V" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1758 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 16, 'TRANS': 210} Chain: "J" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 27, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "K" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "W" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "X" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "Y" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "Z" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 21.77, per 1000 atoms: 0.45 Number of scatterers: 48906 At special positions: 0 Unit cell: (167.575, 164.353, 236.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 170 15.00 O 9743 8.00 N 9012 7.00 C 29935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 8.80 Conformation dependent library (CDL) restraints added in 4.7 seconds 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10474 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 95 sheets defined 34.4% alpha, 20.7% beta 30 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 13.74 Creating SS restraints... Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.933A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.665A pdb=" N LEU B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.838A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 121' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.715A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.793A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.049A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.828A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.622A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.757A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.545A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.554A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 removed outlier: 3.549A pdb=" N LEU F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.758A pdb=" N LEU F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.560A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.606A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 63 through 72 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.522A pdb=" N ARG H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.679A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 removed outlier: 3.684A pdb=" N LEU I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 removed outlier: 3.977A pdb=" N LEU I 112 " --> pdb=" O ASN I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 131 Processing helix chain 'L' and resid 33 through 48 removed outlier: 4.120A pdb=" N PHE L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 116 through 121 removed outlier: 3.853A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS L 121 " --> pdb=" O GLY L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 116 through 121' Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 165 through 178 Processing helix chain 'L' and resid 189 through 201 Processing helix chain 'L' and resid 207 through 215 removed outlier: 3.543A pdb=" N ASP L 211 " --> pdb=" O ALA L 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP L 215 " --> pdb=" O ASP L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 295 removed outlier: 3.737A pdb=" N VAL L 295 " --> pdb=" O PRO L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 302 removed outlier: 4.063A pdb=" N LEU L 301 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU L 302 " --> pdb=" O SER L 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 36 removed outlier: 3.768A pdb=" N SER M 36 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 129 Processing helix chain 'M' and resid 131 through 144 Processing helix chain 'M' and resid 189 through 204 Processing helix chain 'M' and resid 256 through 265 Processing helix chain 'M' and resid 303 through 313 Processing helix chain 'M' and resid 319 through 333 Processing helix chain 'N' and resid 32 through 36 removed outlier: 3.649A pdb=" N SER N 36 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 73 removed outlier: 3.711A pdb=" N SER N 73 " --> pdb=" O ALA N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 129 Processing helix chain 'N' and resid 131 through 144 Processing helix chain 'N' and resid 189 through 204 Processing helix chain 'N' and resid 256 through 265 Processing helix chain 'N' and resid 303 through 313 Processing helix chain 'N' and resid 319 through 333 Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.588A pdb=" N ARG O 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 Processing helix chain 'O' and resid 111 through 129 Processing helix chain 'O' and resid 131 through 144 Processing helix chain 'O' and resid 189 through 204 Processing helix chain 'O' and resid 256 through 265 Processing helix chain 'O' and resid 303 through 313 Processing helix chain 'O' and resid 319 through 333 Processing helix chain 'P' and resid 32 through 36 removed outlier: 3.704A pdb=" N SER P 36 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 72 removed outlier: 3.870A pdb=" N LEU P 67 " --> pdb=" O ASP P 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP P 68 " --> pdb=" O PRO P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 129 Processing helix chain 'P' and resid 131 through 144 Processing helix chain 'P' and resid 189 through 204 Processing helix chain 'P' and resid 256 through 265 Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 319 through 333 Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.660A pdb=" N SER Q 36 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.658A pdb=" N SER Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 129 Processing helix chain 'Q' and resid 131 through 144 Processing helix chain 'Q' and resid 189 through 204 Processing helix chain 'Q' and resid 256 through 265 Processing helix chain 'Q' and resid 303 through 313 Processing helix chain 'Q' and resid 319 through 333 Processing helix chain 'R' and resid 32 through 36 removed outlier: 3.556A pdb=" N SER R 36 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 62 removed outlier: 4.111A pdb=" N ARG R 62 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 72 Processing helix chain 'R' and resid 111 through 129 Processing helix chain 'R' and resid 131 through 144 Processing helix chain 'R' and resid 189 through 204 Processing helix chain 'R' and resid 256 through 265 Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'R' and resid 319 through 333 Processing helix chain 'S' and resid 16 through 36 Processing helix chain 'S' and resid 63 through 72 removed outlier: 3.666A pdb=" N LEU S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA S 72 " --> pdb=" O ARG S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 121 removed outlier: 4.061A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS S 120 " --> pdb=" O LEU S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 131 Processing helix chain 'S' and resid 132 through 136 removed outlier: 3.543A pdb=" N VAL S 135 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA S 136 " --> pdb=" O ASP S 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 132 through 136' Processing helix chain 'U' and resid 47 through 70 removed outlier: 3.673A pdb=" N PHE U 55 " --> pdb=" O VAL U 51 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE U 58 " --> pdb=" O GLU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 136 Processing helix chain 'U' and resid 140 through 147 removed outlier: 3.542A pdb=" N ILE U 143 " --> pdb=" O LEU U 140 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU U 147 " --> pdb=" O THR U 144 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 Processing helix chain 'U' and resid 180 through 188 Processing helix chain 'U' and resid 191 through 197 Processing helix chain 'U' and resid 198 through 200 No H-bonds generated for 'chain 'U' and resid 198 through 200' Processing helix chain 'U' and resid 211 through 222 Processing helix chain 'V' and resid 47 through 70 removed outlier: 3.673A pdb=" N PHE V 55 " --> pdb=" O VAL V 51 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP V 57 " --> pdb=" O ASP V 53 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE V 58 " --> pdb=" O GLU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 136 Processing helix chain 'V' and resid 140 through 147 removed outlier: 3.542A pdb=" N ILE V 143 " --> pdb=" O LEU V 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU V 147 " --> pdb=" O THR V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 168 Processing helix chain 'V' and resid 180 through 189 Processing helix chain 'V' and resid 191 through 197 Processing helix chain 'V' and resid 198 through 200 No H-bonds generated for 'chain 'V' and resid 198 through 200' Processing helix chain 'V' and resid 211 through 222 Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 36 through 61 removed outlier: 7.071A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.543A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.662A pdb=" N ALA A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.564A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.806A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.941A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.607A pdb=" N GLY A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 433 removed outlier: 3.534A pdb=" N GLN A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 31 removed outlier: 3.532A pdb=" N GLY X 27 " --> pdb=" O GLU X 23 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS X 28 " --> pdb=" O ARG X 24 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS X 31 " --> pdb=" O GLY X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 61 removed outlier: 7.071A pdb=" N LEU X 53 " --> pdb=" O ARG X 49 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA X 54 " --> pdb=" O GLU X 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 126 removed outlier: 3.541A pdb=" N VAL X 117 " --> pdb=" O ALA X 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN X 126 " --> pdb=" O SER X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 134 Processing helix chain 'X' and resid 138 through 146 removed outlier: 3.661A pdb=" N ALA X 144 " --> pdb=" O GLU X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 164 Processing helix chain 'X' and resid 196 through 211 Processing helix chain 'X' and resid 212 through 225 Processing helix chain 'X' and resid 247 through 251 removed outlier: 3.805A pdb=" N ASN X 250 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE X 251 " --> pdb=" O PRO X 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 247 through 251' Processing helix chain 'X' and resid 253 through 258 Processing helix chain 'X' and resid 282 through 290 Processing helix chain 'X' and resid 294 through 307 removed outlier: 3.942A pdb=" N LEU X 307 " --> pdb=" O THR X 303 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 344 Processing helix chain 'X' and resid 355 through 361 Processing helix chain 'X' and resid 372 through 382 Processing helix chain 'X' and resid 384 through 399 removed outlier: 3.607A pdb=" N GLY X 388 " --> pdb=" O PRO X 384 " (cutoff:3.500A) Processing helix chain 'X' and resid 402 through 407 Processing helix chain 'X' and resid 409 through 433 removed outlier: 3.534A pdb=" N GLN X 413 " --> pdb=" O PRO X 409 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU X 432 " --> pdb=" O ILE X 428 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG X 433 " --> pdb=" O LEU X 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.941A pdb=" N GLY B 112 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY B 58 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 57 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS B 305 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.941A pdb=" N GLY B 112 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY B 58 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 57 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N HIS B 305 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 278 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.697A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 240 through 242 removed outlier: 4.419A pdb=" N ARG B 218 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 removed outlier: 5.051A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB2, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.868A pdb=" N LYS C 293 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.817A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 49 Processing sheet with id=AB7, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.541A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 109 Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.493A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.875A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER E 243 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.522A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 109 Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.863A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'F' and resid 45 through 51 removed outlier: 7.537A pdb=" N SER F 243 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 78 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC9, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD1, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.631A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.942A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 50 Processing sheet with id=AD5, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD6, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.509A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.786A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.177A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.177A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS U 26 " --> pdb=" O THR U 41 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR U 41 " --> pdb=" O HIS U 26 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP U 28 " --> pdb=" O ILE U 39 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE U 39 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU U 30 " --> pdb=" O MET U 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE4, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AE5, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AE6, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AE7, first strand: chain 'I' and resid 100 through 102 Processing sheet with id=AE8, first strand: chain 'I' and resid 172 through 173 removed outlier: 3.760A pdb=" N GLY I 172 " --> pdb=" O LYS I 180 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.005A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.005A pdb=" N GLY L 58 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY L 112 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA L 103 " --> pdb=" O GLN L 18 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLN L 18 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU L 105 " --> pdb=" O SER L 16 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER L 16 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL L 107 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG L 14 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 70 through 71 Processing sheet with id=AF3, first strand: chain 'L' and resid 185 through 188 removed outlier: 7.146A pdb=" N PHE L 279 " --> pdb=" O ALA L 257 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA L 257 " --> pdb=" O PHE L 279 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU L 281 " --> pdb=" O TYR L 255 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR L 255 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU L 283 " --> pdb=" O ALA L 253 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP L 247 " --> pdb=" O TRP L 289 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA L 253 " --> pdb=" O TRP L 316 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP L 316 " --> pdb=" O ALA L 253 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 185 through 188 removed outlier: 6.720A pdb=" N ARG L 278 " --> pdb=" O ALA X 191 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 240 through 242 removed outlier: 4.408A pdb=" N ARG L 218 " --> pdb=" O ARG L 242 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE X 232 " --> pdb=" O ILE L 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 108 through 109 Processing sheet with id=AF7, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.054A pdb=" N ALA M 157 " --> pdb=" O ARG M 218 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 19 through 20 removed outlier: 4.894A pdb=" N ALA M 253 " --> pdb=" O MET M 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 44 through 47 Processing sheet with id=AG1, first strand: chain 'M' and resid 266 through 268 Processing sheet with id=AG2, first strand: chain 'N' and resid 108 through 109 removed outlier: 3.556A pdb=" N ALA N 108 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 19 through 20 removed outlier: 4.743A pdb=" N LEU N 210 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL N 158 " --> pdb=" O ASP N 177 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP N 177 " --> pdb=" O VAL N 158 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL N 160 " --> pdb=" O ARG N 175 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG N 175 " --> pdb=" O VAL N 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE N 162 " --> pdb=" O THR N 173 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR N 173 " --> pdb=" O ILE N 162 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS N 164 " --> pdb=" O ALA N 171 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AG5, first strand: chain 'N' and resid 45 through 50 Processing sheet with id=AG6, first strand: chain 'N' and resid 287 through 288 removed outlier: 3.661A pdb=" N LYS N 293 " --> pdb=" O VAL N 288 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 108 through 109 Processing sheet with id=AG8, first strand: chain 'O' and resid 19 through 20 removed outlier: 4.740A pdb=" N LEU O 210 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL O 158 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP O 177 " --> pdb=" O VAL O 158 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL O 160 " --> pdb=" O ARG O 175 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG O 175 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE O 162 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR O 173 " --> pdb=" O ILE O 162 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS O 164 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AH1, first strand: chain 'O' and resid 45 through 50 removed outlier: 7.658A pdb=" N SER O 243 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR O 78 " --> pdb=" O SER O 243 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 287 through 288 removed outlier: 3.504A pdb=" N LYS O 293 " --> pdb=" O VAL O 288 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 108 through 109 removed outlier: 3.506A pdb=" N ALA P 108 " --> pdb=" O ALA P 13 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 19 through 20 removed outlier: 4.751A pdb=" N LEU P 210 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL P 158 " --> pdb=" O ASP P 177 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP P 177 " --> pdb=" O VAL P 158 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL P 160 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG P 175 " --> pdb=" O VAL P 160 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE P 162 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR P 173 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS P 164 " --> pdb=" O ALA P 171 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 19 through 20 Processing sheet with id=AH6, first strand: chain 'P' and resid 45 through 51 removed outlier: 7.477A pdb=" N SER P 243 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR P 78 " --> pdb=" O SER P 243 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 287 through 288 Processing sheet with id=AH8, first strand: chain 'Q' and resid 108 through 109 removed outlier: 3.519A pdb=" N ALA Q 108 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 20 removed outlier: 4.574A pdb=" N LEU Q 210 " --> pdb=" O ILE Q 165 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA Q 157 " --> pdb=" O ARG Q 218 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL Q 158 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP Q 177 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL Q 160 " --> pdb=" O ARG Q 175 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG Q 175 " --> pdb=" O VAL Q 160 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE Q 162 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR Q 173 " --> pdb=" O ILE Q 162 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS Q 164 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AI2, first strand: chain 'Q' and resid 45 through 51 removed outlier: 4.046A pdb=" N ASN Q 75 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 287 through 288 Processing sheet with id=AI4, first strand: chain 'R' and resid 108 through 109 Processing sheet with id=AI5, first strand: chain 'R' and resid 19 through 20 removed outlier: 4.425A pdb=" N LEU R 210 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL R 158 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP R 177 " --> pdb=" O VAL R 158 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL R 160 " --> pdb=" O ARG R 175 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG R 175 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE R 162 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR R 173 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS R 164 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AI7, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.345A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 44 through 51 removed outlier: 4.345A pdb=" N ASN R 75 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS V 26 " --> pdb=" O THR V 41 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR V 41 " --> pdb=" O HIS V 26 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP V 28 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE V 39 " --> pdb=" O TRP V 28 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU V 30 " --> pdb=" O MET V 37 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 266 through 268 Processing sheet with id=AJ1, first strand: chain 'R' and resid 287 through 288 removed outlier: 3.751A pdb=" N VAL R 288 " --> pdb=" O LYS R 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS R 293 " --> pdb=" O VAL R 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ3, first strand: chain 'S' and resid 41 through 43 Processing sheet with id=AJ4, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AJ5, first strand: chain 'S' and resid 100 through 102 Processing sheet with id=AJ6, first strand: chain 'S' and resid 172 through 173 removed outlier: 3.514A pdb=" N GLY S 172 " --> pdb=" O LYS S 180 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.514A pdb=" N LEU U 77 " --> pdb=" O LEU U 86 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG U 88 " --> pdb=" O LEU U 75 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU U 75 " --> pdb=" O ARG U 88 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA U 90 " --> pdb=" O ASP U 73 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP U 73 " --> pdb=" O ALA U 90 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'V' and resid 85 through 91 removed outlier: 6.515A pdb=" N LEU V 77 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG V 88 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU V 75 " --> pdb=" O ARG V 88 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA V 90 " --> pdb=" O ASP V 73 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP V 73 " --> pdb=" O ALA V 90 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AK1, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AK2, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AK3, first strand: chain 'X' and resid 65 through 66 Processing sheet with id=AK4, first strand: chain 'X' and resid 68 through 69 Processing sheet with id=AK5, first strand: chain 'X' and resid 239 through 242 2195 hydrogen bonds defined for protein. 5991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 20.66 Time building geometry restraints manager: 10.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9736 1.32 - 1.45: 12927 1.45 - 1.57: 27171 1.57 - 1.69: 338 1.69 - 1.81: 71 Bond restraints: 50243 Sorted by residual: bond pdb=" CA ASN B 149 " pdb=" C ASN B 149 " ideal model delta sigma weight residual 1.523 1.576 -0.053 1.34e-02 5.57e+03 1.57e+01 bond pdb=" C ARG V 93 " pdb=" N LEU V 94 " ideal model delta sigma weight residual 1.333 1.263 0.070 2.74e-02 1.33e+03 6.53e+00 bond pdb=" C ARG U 93 " pdb=" N LEU U 94 " ideal model delta sigma weight residual 1.333 1.263 0.069 2.74e-02 1.33e+03 6.39e+00 bond pdb=" C PHE E 336 " pdb=" N GLY E 337 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.46e-02 4.69e+03 4.26e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.08e+00 ... (remaining 50238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 65842 1.81 - 3.61: 2620 3.61 - 5.42: 327 5.42 - 7.22: 67 7.22 - 9.03: 27 Bond angle restraints: 68883 Sorted by residual: angle pdb=" N LEU L 181 " pdb=" CA LEU L 181 " pdb=" C LEU L 181 " ideal model delta sigma weight residual 112.35 121.25 -8.90 1.34e+00 5.57e-01 4.42e+01 angle pdb=" N ALA E 339 " pdb=" CA ALA E 339 " pdb=" C ALA E 339 " ideal model delta sigma weight residual 111.30 104.37 6.93 1.43e+00 4.89e-01 2.35e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 108.58 101.83 6.75 1.44e+00 4.82e-01 2.20e+01 angle pdb=" N LYS E 238 " pdb=" CA LYS E 238 " pdb=" C LYS E 238 " ideal model delta sigma weight residual 112.92 118.56 -5.64 1.23e+00 6.61e-01 2.10e+01 angle pdb=" C ALA U 205 " pdb=" N ASN U 206 " pdb=" CA ASN U 206 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+01 ... (remaining 68878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 28039 35.06 - 70.12: 1111 70.12 - 105.19: 104 105.19 - 140.25: 6 140.25 - 175.31: 10 Dihedral angle restraints: 29270 sinusoidal: 12468 harmonic: 16802 Sorted by residual: dihedral pdb=" O4' U J 33 " pdb=" C1' U J 33 " pdb=" N1 U J 33 " pdb=" C2 U J 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.46 147.54 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U T 33 " pdb=" C1' U T 33 " pdb=" N1 U T 33 " pdb=" C2 U T 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.53 147.47 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' U T 21 " pdb=" C1' U T 21 " pdb=" N1 U T 21 " pdb=" C2 U T 21 " ideal model delta sinusoidal sigma weight residual 200.00 63.24 136.76 1 1.50e+01 4.44e-03 7.37e+01 ... (remaining 29267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 7163 0.108 - 0.216: 335 0.216 - 0.324: 9 0.324 - 0.433: 1 0.433 - 0.541: 3 Chirality restraints: 7511 Sorted by residual: chirality pdb=" CB VAL X 199 " pdb=" CA VAL X 199 " pdb=" CG1 VAL X 199 " pdb=" CG2 VAL X 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CB VAL A 199 " pdb=" CA VAL A 199 " pdb=" CG1 VAL A 199 " pdb=" CG2 VAL A 199 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CB ILE S 40 " pdb=" CA ILE S 40 " pdb=" CG1 ILE S 40 " pdb=" CG2 ILE S 40 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 7508 not shown) Planarity restraints: 8618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 248 " 0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C SER F 248 " -0.072 2.00e-02 2.50e+03 pdb=" O SER F 248 " 0.028 2.00e-02 2.50e+03 pdb=" N VAL F 249 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO A 270 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO X 269 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO X 270 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO X 270 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO X 270 " 0.042 5.00e-02 4.00e+02 ... (remaining 8615 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 635 2.62 - 3.19: 40569 3.19 - 3.76: 77693 3.76 - 4.33: 108202 4.33 - 4.90: 174557 Nonbonded interactions: 401656 Sorted by model distance: nonbonded pdb=" O ASN U 2 " pdb=" OD1 ASN U 2 " model vdw 2.049 3.040 nonbonded pdb=" O ASN V 2 " pdb=" OD1 ASN V 2 " model vdw 2.052 3.040 nonbonded pdb=" CD1 LEU L 181 " pdb=" CD PRO L 182 " model vdw 2.086 3.860 nonbonded pdb=" N1 DG K 42 " pdb=" O6 DG W 2 " model vdw 2.104 3.120 nonbonded pdb=" OG SER U 191 " pdb=" OD1 ASN U 194 " model vdw 2.214 3.040 ... (remaining 401651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'X' } ncs_group { reference = (chain 'B' and (resid 3 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 75 or (resid 76 through 77 a \ nd (name N or name CA or name C or name O or name CB )) or resid 78 through 149 \ or (resid 150 through 151 and (name N or name CA or name C or name O or name CB \ )) or resid 152 through 166 or (resid 167 and (name N or name CA or name C or na \ me O or name CB )) or resid 168 through 188 or (resid 189 through 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 239 or (resi \ d 240 and (name N or name CA or name C or name O or name CB )) or resid 241 thro \ ugh 285 or (resid 286 and (name N or name CA or name C or name O or name CB )) o \ r resid 287 through 322)) selection = (chain 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name \ O or name CB )) or resid 15 through 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 51 or (resid 52 and (name N or \ name CA or name C or name O or name CB )) or resid 53 through 62 or (resid 63 an \ d (name N or name CA or name C or name O or name CB )) or resid 64 through 66 or \ (resid 67 through 68 and (name N or name CA or name C or name O or name CB )) o \ r resid 69 through 76 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 93 or (resid 94 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 107 or (resid 108 and (n \ ame N or name CA or name C or name O or name CB )) or resid 109 through 112 or ( \ resid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 \ through 120 or (resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 127 or (resid 128 and (name N or name CA or name C or na \ me O or name CB )) or resid 129 through 146 or (resid 147 and (name N or name CA \ or name C or name O or name CB )) or resid 148 through 157 or (resid 158 and (n \ ame N or name CA or name C or name O or name CB )) or resid 159 through 160 or ( \ resid 161 through 162 and (name N or name CA or name C or name O or name CB )) o \ r resid 163 through 168 or (resid 169 through 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 or (resid 172 through 173 and (name N or \ name CA or name C or name O or name CB )) or resid 174 or (resid 175 and (name \ N or name CA or name C or name O or name CB )) or resid 176 through 177 or (resi \ d 178 and (name N or name CA or name C or name O or name CB )) or resid 179 thro \ ugh 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) o \ r resid 193 through 197 or (resid 198 and (name N or name CA or name C or name O \ or name CB )) or resid 199 through 209 or (resid 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 213 or (resid 214 and (name \ N or name CA or name C or name O or name CB )) or resid 215 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 239 through 240 and (name N or name CA or name C or name O or \ name CB )) or resid 241 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 276 or (resid 277 and (name N or \ name CA or name C or name O or name CB )) or resid 278 through 281 or (resid 28 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 283 through \ 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or re \ sid 291 through 300 or (resid 301 and (name N or name CA or name C or name O or \ name CB )) or resid 302 through 304 or (resid 305 and (name N or name CA or name \ C or name O or name CB )) or resid 306 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 319 or (resid 32 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 321 through \ 322)) } ncs_group { reference = (chain 'C' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 through 48 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 79 or (re \ sid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thro \ ugh 97 or (resid 98 and (name N or name CA or name C or name O or name CB )) or \ resid 99 through 108 or (resid 109 through 110 and (name N or name CA or name C \ or name O 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 name CB )) or resid 331 through 337 or (resid 3 \ 38 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' 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 through 161 or (resid 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 228 or (resid 229 and (name N or name CA or name C or name O or name \ CB )) or resid 230 or (resid 231 and (name N or name CA or name C or name O or n \ ame CB )) or resid 244 through 245 or (resid 246 and (name N or name CA or name \ C or name O or name CB )) or resid 247 through 249 or (resid 250 and (name N or \ name CA or name C or name O or name CB )) or resid 251 through 270 or (resid 271 \ and (name N or name CA or name C or name O or name CB )) or resid 272 through 2 \ 76 or (resid 277 and (name N or name CA or name C or name O or name CB )) or res \ id 278 through 282 or (resid 283 and (name N or name CA or name C or name O or n \ ame 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 n \ ame 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 throu \ gh 301 or (resid 302 through 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 304 through 306 or (resid 307 and (name N or name CA or name \ C or name O or name CB )) or resid 308 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 320 or (resid 321 \ and (name N or name CA or name C 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or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame CB )) or resid 278 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )) or resid 284 or (resid 285 and (name N or name CA or n \ ame C or name O or name CB )) or resid 286 through 290 or (resid 291 and (name N \ or name CA or name C or name O or name CB )) or resid 292 through 295 or (resid \ 296 through 297 and (name N or name CA or name C or name O or name CB )) or res \ id 298 or (resid 299 and (name N or name CA or name C or name O or name CB )) or \ resid 300 through 301 or (resid 302 through 303 and (name N or name CA or name \ C or name O or name CB )) or resid 304 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 through 313 or (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 20 or (resid 321 and (name N or name CA or name C or name O or name CB )) or res \ id 322 through 323 or (resid 324 and (name N or name CA or name C or name O or n \ ame CB )) or resid 325 through 326 or (resid 327 through 328 and (name N or name \ CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name N or \ name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 338 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame CB )) or resid 278 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )) or resid 284 or (resid 285 and (name N or name CA or n \ ame C or name O or name CB )) or resid 286 through 290 or (resid 291 and (name N \ or name CA or name C or name O or name CB )) or resid 292 through 295 or (resid \ 296 through 297 and (name N or name CA or name C or name O or name CB )) or res \ id 298 or (resid 299 and (name N or name CA or name C or name O or name CB )) or \ resid 300 through 301 or (resid 302 through 303 and (name N or name CA or name \ C or name O or name CB )) or resid 304 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 through 313 or (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 20 or (resid 321 and (name N or name CA or name C or name O or name CB )) or res \ id 322 through 323 or (resid 324 and (name N or name CA or name C or name O or n \ ame CB )) or resid 325 through 326 or (resid 327 through 328 and (name N or name \ CA or name C or name O or name CB )) or resid 329 or (resid 330 and (name N or \ name CA or name C or name O or name CB )) or resid 331 through 337 or (resid 338 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame CB )) or resid 278 through 284 or (resid 285 and (name N or name CA or name \ C or name O or name CB )) or resid 286 through 290 or (resid 291 and (name N or \ name CA or name C or name O or name CB )) or resid 292 through 295 or (resid 296 \ through 297 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 98 or (resid 299 and (name N or name CA or name C or name O or name CB )) or res \ id 300 through 301 or (resid 302 through 303 and (name N or name CA or name C or \ name O or name CB )) or resid 304 through 306 or (resid 307 and (name N or name \ CA or name C or name O or name CB )) or resid 308 through 313 or (resid 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 320 o \ r (resid 321 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 22 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 326 or (resid 327 through 328 and (name N or name CA \ or name C or name O or name CB )) or resid 329 or (resid 330 and (name N or name \ CA or name C or name O or name CB )) or resid 331 through 337 or (resid 338 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 108 or (r \ esid 109 through 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 or (resid 117 through 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 130 or (resid 131 \ through 133 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 34 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or \ name O or name CB )) or resid 141 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 155 or (resid 156 thr \ ough 157 and (name N or name CA or name C or name O or name CB )) or resid 158 o \ r (resid 159 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 60 or (resid 161 through 162 and (name N or name CA or name C or name O or name \ CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name O or n \ ame CB )) or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 or (r \ esid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 70 or (resid 271 and (name N or name CA or name C or name O or name CB )) or res \ id 272 through 276 or (resid 277 and (name N or name CA or name C or name O or n \ ame CB )) or resid 278 through 282 or (resid 283 and (name N or name CA or name \ C or name O or name CB )) or resid 284 or (resid 285 and (name N or name CA or n \ ame C or name O or name CB )) or resid 286 through 290 or (resid 291 and (name N \ or name CA or name C or name O or name CB )) or resid 292 through 295 or (resid \ 296 through 297 and (name N or name CA or name C or name O or name CB )) or res \ id 298 or (resid 299 and (name N or name CA or name C or name O or name CB )) or \ resid 300 through 301 or (resid 302 through 303 and (name N or name CA or name \ C or name O or name CB )) or resid 304 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 through 313 or (resid 314 \ and (name N or name CA or name C or name O or name CB )) or resid 315 through 3 \ 23 or (resid 324 and (name N or name CA or name C or name O or name CB )) or res \ id 325 through 326 or (resid 327 through 328 and (name N or name CA or name C or \ name O or name CB )) or resid 329 or (resid 330 and (name N or name CA or name \ C or name O or name CB )) or resid 331 through 337 or (resid 338 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 7 or (resid 8 through 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 14 or (resid 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 or (resid 17 and (name N or name \ CA or name C or name O or name CB )) or resid 18 or (resid 19 and (name N or na \ me CA or name C or name O or name CB )) or resid 20 through 32 or (resid 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 through 36 or ( \ resid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 th \ rough 44 or (resid 45 and (name N or name CA or name C or name O or name CB )) o \ r resid 46 through 48 or (resid 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 113 or (r \ esid 114 through 115 and (name N or name CA or name C or name O or name CB )) or \ resid 116 or (resid 117 through 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 through 130 or (resid 131 through 133 and (name N or \ name CA or name C or name O or name CB )) or resid 134 through 135 or (resid 136 \ and (name N or name CA or name C or name O or name CB )) or resid 137 through 1 \ 39 or (resid 140 and (name N or name CA or name C or name O or name CB )) or res \ id 141 through 149 or (resid 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 155 or (resid 156 through 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 or (resid 159 and (name N or \ name CA or name C or name O or name CB )) or resid 160 or (resid 161 through 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throu \ gh 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or \ resid 170 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 207 or (resid 208 and (name N or name CA or n \ ame C or name O or name CB )) or resid 209 or (resid 210 and (name N or name CA \ or name C or name O or name CB )) or resid 211 through 217 or (resid 218 and (na \ me N or name CA or name C or name O or name CB )) or resid 219 through 228 or (r \ esid 229 and (name N or name CA or name C or name O or name CB )) or resid 230 o \ r (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 44 through 245 or (resid 246 and (name N or name CA or name C or name O or name \ CB )) or resid 247 through 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB )) or resid 251 through 270 or (resid 271 and (name N or name \ CA or name C or name O or name CB )) or resid 272 through 276 or (resid 277 and \ (name N or name CA or name C or name O or name CB )) or resid 278 through 282 o \ r (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 84 or (resid 285 and (name N or name CA or name C or name O or name CB )) or res \ id 286 through 290 or (resid 291 and (name N or name CA or name C or name O or n \ ame CB )) or resid 292 through 295 or (resid 296 through 297 and (name N or name \ CA or name C or name O or name CB )) or resid 298 or (resid 299 and (name N or \ name CA or name C or name O or name CB )) or resid 300 through 301 or (resid 302 \ through 303 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 04 through 306 or (resid 307 and (name N or name CA or name C or name O or name \ CB )) or resid 308 through 313 or (resid 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 320 or (resid 321 and (name N or name \ CA or name C or name O or name CB )) or resid 322 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 329 o \ r (resid 330 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 31 through 337 or (resid 338 and (name N or name CA or name C or name O or name \ CB )))) } ncs_group { reference = (chain 'I' and (resid 1 through 174 or resid 176 through 177 or (resid 178 and ( \ name N or name CA or name C or name O or name CB )) or resid 179 through 187)) selection = (chain 'S' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.080 Extract box with map and model: 1.430 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 94.470 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 50243 Z= 0.487 Angle : 0.837 9.031 68883 Z= 0.481 Chirality : 0.052 0.541 7511 Planarity : 0.006 0.075 8618 Dihedral : 17.897 175.310 18796 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 0.58 % Allowed : 11.71 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.09), residues: 6156 helix: -2.28 (0.08), residues: 1977 sheet: -0.13 (0.15), residues: 1050 loop : -2.54 (0.09), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 174 HIS 0.010 0.002 HIS S 3 PHE 0.022 0.002 PHE L 152 TYR 0.022 0.002 TYR P 271 ARG 0.010 0.001 ARG S 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 468 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 PHE cc_start: 0.7827 (m-80) cc_final: 0.7590 (m-80) REVERT: C 221 ASP cc_start: 0.8104 (m-30) cc_final: 0.7748 (t0) REVERT: C 223 GLN cc_start: 0.6666 (mp10) cc_final: 0.5715 (mt0) REVERT: C 277 LEU cc_start: 0.3769 (pp) cc_final: 0.3538 (mm) REVERT: H 167 GLN cc_start: 0.8183 (tp40) cc_final: 0.7881 (tp40) REVERT: I 21 MET cc_start: 0.2383 (ptt) cc_final: 0.1537 (tpp) REVERT: L 171 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8249 (ptpp) REVERT: L 174 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7926 (ttp-170) REVERT: M 197 GLU cc_start: 0.7720 (tp30) cc_final: 0.7480 (tp30) REVERT: M 219 ILE cc_start: 0.8285 (mp) cc_final: 0.8021 (mp) REVERT: P 46 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7656 (mt-10) REVERT: R 299 LYS cc_start: 0.8807 (ptmt) cc_final: 0.8604 (mmmt) REVERT: A 207 ARG cc_start: 0.8228 (ptp-110) cc_final: 0.7878 (ptm-80) REVERT: A 241 GLN cc_start: 0.8319 (tt0) cc_final: 0.8004 (tt0) REVERT: X 253 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7706 (tp40) outliers start: 25 outliers final: 17 residues processed: 487 average time/residue: 1.5012 time to fit residues: 886.0269 Evaluate side-chains 274 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain X residue 211 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 529 optimal weight: 2.9990 chunk 475 optimal weight: 20.0000 chunk 263 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 320 optimal weight: 0.4980 chunk 253 optimal weight: 2.9990 chunk 491 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 365 optimal weight: 0.9980 chunk 569 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 82 ASN B 129 GLN B 131 GLN B 196 HIS C 120 GLN C 127 ASN D 75 ASN D 291 GLN E 241 GLN G 72 GLN G 120 GLN I 3 HIS I 35 GLN I 99 GLN I 165 GLN L 129 GLN L 131 GLN ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 GLN N 120 GLN N 291 GLN O 120 GLN O 223 GLN P 291 GLN Q 120 GLN R 120 GLN S 3 HIS S 19 GLN S 35 GLN S 82 HIS ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS X 64 GLN X 68 HIS ** X 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 230 HIS X 253 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50243 Z= 0.187 Angle : 0.552 9.240 68883 Z= 0.299 Chirality : 0.040 0.166 7511 Planarity : 0.004 0.057 8618 Dihedral : 17.129 178.088 9196 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.97 % Allowed : 15.68 % Favored : 82.35 % 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: -1.52 (0.10), residues: 6156 helix: -0.12 (0.10), residues: 1991 sheet: 0.21 (0.15), residues: 1041 loop : -2.10 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 174 HIS 0.013 0.001 HIS X 188 PHE 0.012 0.001 PHE A 232 TYR 0.014 0.001 TYR R 114 ARG 0.015 0.001 ARG L 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 315 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8823 (m) cc_final: 0.8371 (p) REVERT: B 284 PHE cc_start: 0.7764 (m-80) cc_final: 0.7474 (m-80) REVERT: C 87 ASP cc_start: 0.7206 (p0) cc_final: 0.6707 (t0) REVERT: C 174 TRP cc_start: 0.7530 (m-90) cc_final: 0.6801 (m-90) REVERT: C 221 ASP cc_start: 0.8138 (m-30) cc_final: 0.7724 (t0) REVERT: C 223 GLN cc_start: 0.6571 (mp10) cc_final: 0.5687 (mt0) REVERT: C 293 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7812 (tptp) REVERT: I 21 MET cc_start: 0.2567 (ptt) cc_final: 0.1670 (mtt) REVERT: L 171 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8130 (ptpt) REVERT: L 321 PHE cc_start: 0.6813 (p90) cc_final: 0.6292 (t80) REVERT: M 264 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8230 (tm) REVERT: N 50 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7528 (ptp90) REVERT: U 127 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: V 46 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: V 209 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8782 (mmmm) REVERT: A 59 ARG cc_start: 0.6576 (mmp80) cc_final: 0.5187 (mmt90) REVERT: A 81 ASN cc_start: 0.6630 (p0) cc_final: 0.6142 (p0) REVERT: A 207 ARG cc_start: 0.8263 (ptp-110) cc_final: 0.7878 (ptm-80) REVERT: X 253 GLN cc_start: 0.7634 (tp40) cc_final: 0.6877 (tp40) outliers start: 85 outliers final: 29 residues processed: 377 average time/residue: 1.2978 time to fit residues: 610.4829 Evaluate side-chains 301 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 77 GLN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 120 GLN Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 316 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 473 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 570 optimal weight: 20.0000 chunk 616 optimal weight: 0.3980 chunk 508 optimal weight: 4.9990 chunk 565 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 457 optimal weight: 4.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN D 208 HIS E 72 GLN E 164 HIS F 120 GLN F 127 ASN ** L 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN M 140 HIS N 208 HIS Q 120 GLN Q 291 GLN R 140 HIS ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 200 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 50243 Z= 0.479 Angle : 0.655 14.712 68883 Z= 0.349 Chirality : 0.045 0.193 7511 Planarity : 0.005 0.055 8618 Dihedral : 17.099 177.983 9179 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.76 % Allowed : 17.30 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.10), residues: 6156 helix: 0.67 (0.11), residues: 2016 sheet: 0.20 (0.15), residues: 1049 loop : -1.92 (0.10), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 311 HIS 0.010 0.002 HIS G 256 PHE 0.021 0.002 PHE C 95 TYR 0.020 0.002 TYR O 271 ARG 0.017 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 275 time to evaluate : 4.081 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: B 177 THR cc_start: 0.8826 (m) cc_final: 0.8393 (p) REVERT: B 284 PHE cc_start: 0.7829 (m-80) cc_final: 0.7587 (m-80) REVERT: C 117 LYS cc_start: 0.6725 (tptp) cc_final: 0.6482 (tptt) REVERT: C 223 GLN cc_start: 0.6496 (mp10) cc_final: 0.5425 (mt0) REVERT: C 285 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: C 293 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7829 (tmtt) REVERT: C 301 LYS cc_start: 0.8400 (mmtm) cc_final: 0.7919 (ttmm) REVERT: E 283 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: H 34 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7544 (OUTLIER) REVERT: I 21 MET cc_start: 0.2776 (ptt) cc_final: 0.1751 (tpp) REVERT: L 171 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8204 (ptpt) REVERT: L 174 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7171 (ttp-170) REVERT: L 321 PHE cc_start: 0.7067 (p90) cc_final: 0.6012 (t80) REVERT: M 264 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8178 (tm) REVERT: S 21 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4174 (pp-130) REVERT: U 37 MET cc_start: 0.8451 (mtp) cc_final: 0.8209 (mtp) REVERT: U 127 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: V 46 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: V 209 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8674 (mmmm) REVERT: A 59 ARG cc_start: 0.6114 (mmp80) cc_final: 0.5568 (mmt90) REVERT: A 207 ARG cc_start: 0.8262 (ptp-110) cc_final: 0.7919 (ptm-80) REVERT: A 216 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8829 (mmmm) REVERT: A 241 GLN cc_start: 0.8148 (tt0) cc_final: 0.7859 (tt0) REVERT: X 59 ARG cc_start: 0.6646 (mtt180) cc_final: 0.5986 (mmt180) outliers start: 119 outliers final: 57 residues processed: 373 average time/residue: 1.3334 time to fit residues: 619.6196 Evaluate side-chains 297 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 174 ARG Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 77 GLN Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 83 ASP Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 257 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 563 optimal weight: 9.9990 chunk 428 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 383 optimal weight: 2.9990 chunk 572 optimal weight: 30.0000 chunk 606 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 542 optimal weight: 9.9990 chunk 163 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 196 HIS ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN L 133 GLN ** L 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 50243 Z= 0.270 Angle : 0.559 12.243 68883 Z= 0.298 Chirality : 0.041 0.312 7511 Planarity : 0.004 0.051 8618 Dihedral : 16.946 179.692 9175 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.23 % Allowed : 18.77 % Favored : 79.01 % 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: -0.56 (0.10), residues: 6156 helix: 1.19 (0.11), residues: 2004 sheet: 0.26 (0.15), residues: 1090 loop : -1.75 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 174 HIS 0.005 0.001 HIS G 256 PHE 0.012 0.001 PHE L 152 TYR 0.023 0.002 TYR C 114 ARG 0.010 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 275 time to evaluate : 3.983 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: B 177 THR cc_start: 0.8771 (m) cc_final: 0.8470 (p) REVERT: B 284 PHE cc_start: 0.7763 (m-80) cc_final: 0.7533 (m-80) REVERT: C 223 GLN cc_start: 0.6428 (mp10) cc_final: 0.5437 (mt0) REVERT: C 285 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: C 301 LYS cc_start: 0.8356 (mmtm) cc_final: 0.7856 (ttmm) REVERT: G 58 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7810 (ttmm) REVERT: H 125 TYR cc_start: 0.7647 (t80) cc_final: 0.6484 (t80) REVERT: H 314 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7697 (mpp80) REVERT: I 21 MET cc_start: 0.3030 (ptt) cc_final: 0.1970 (tpp) REVERT: L 161 MET cc_start: 0.6817 (pmm) cc_final: 0.5952 (pmm) REVERT: L 171 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8198 (ptpt) REVERT: L 174 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7314 (ttp-170) REVERT: L 321 PHE cc_start: 0.7156 (p90) cc_final: 0.6089 (t80) REVERT: M 264 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8199 (tm) REVERT: R 314 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.7096 (mpp80) REVERT: S 2 ASP cc_start: 0.6803 (t70) cc_final: 0.6468 (p0) REVERT: S 121 ASP cc_start: 0.4051 (m-30) cc_final: 0.3218 (p0) REVERT: U 37 MET cc_start: 0.8408 (mtp) cc_final: 0.8188 (mtp) REVERT: U 127 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: V 46 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: V 209 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8551 (mmmm) REVERT: A 65 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7732 (mp) REVERT: A 207 ARG cc_start: 0.8287 (ptp-110) cc_final: 0.7925 (ptm-80) REVERT: A 208 GLU cc_start: 0.8249 (tp30) cc_final: 0.7962 (tp30) REVERT: A 241 GLN cc_start: 0.8094 (tt0) cc_final: 0.7796 (tt0) REVERT: X 59 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6029 (mmt180) outliers start: 96 outliers final: 51 residues processed: 356 average time/residue: 1.2983 time to fit residues: 579.7427 Evaluate side-chains 300 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 174 ARG Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 77 GLN Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 117 MET Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain X residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 504 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 451 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 517 optimal weight: 0.9980 chunk 418 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 309 optimal weight: 5.9990 chunk 543 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN F 120 GLN ** L 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS S 84 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.007 0.053 50243 Z= 0.437 Angle : 0.632 14.800 68883 Z= 0.336 Chirality : 0.044 0.200 7511 Planarity : 0.004 0.053 8618 Dihedral : 16.955 179.500 9175 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.27 % Allowed : 19.09 % Favored : 77.64 % 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: -0.54 (0.10), residues: 6156 helix: 1.20 (0.11), residues: 2002 sheet: 0.26 (0.15), residues: 1056 loop : -1.71 (0.10), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 147 HIS 0.011 0.001 HIS G 256 PHE 0.019 0.002 PHE C 95 TYR 0.023 0.002 TYR C 114 ARG 0.009 0.001 ARG X 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 262 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7544 (mtm-85) REVERT: B 177 THR cc_start: 0.8650 (m) cc_final: 0.8370 (p) REVERT: B 284 PHE cc_start: 0.7822 (m-80) cc_final: 0.7606 (m-80) REVERT: C 223 GLN cc_start: 0.6383 (mp10) cc_final: 0.5368 (mt0) REVERT: C 285 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.7068 (m-10) REVERT: C 301 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8133 (ttmm) REVERT: E 60 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8864 (ttpt) REVERT: G 58 LYS cc_start: 0.8310 (ttmm) cc_final: 0.8085 (ttmm) REVERT: H 34 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7653 (p0) REVERT: I 21 MET cc_start: 0.3235 (ptt) cc_final: 0.1713 (tpp) REVERT: L 171 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8219 (ptpt) REVERT: L 290 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8843 (pp) REVERT: L 311 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7921 (mtmm) REVERT: M 264 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8202 (tm) REVERT: U 127 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: V 46 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: V 209 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: A 207 ARG cc_start: 0.8257 (ptp-110) cc_final: 0.7888 (ptm-80) REVERT: A 241 GLN cc_start: 0.8158 (tt0) cc_final: 0.7877 (tt0) REVERT: X 59 ARG cc_start: 0.6848 (mtt180) cc_final: 0.6097 (mmt180) REVERT: X 224 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.7988 (tpp-160) outliers start: 141 outliers final: 71 residues processed: 381 average time/residue: 1.3182 time to fit residues: 626.3509 Evaluate side-chains 315 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 235 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 30 TRP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 77 GLN Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 120 GLN Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 83 ASP Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 101 CYS Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 203 optimal weight: 9.9990 chunk 545 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 355 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 606 optimal weight: 7.9990 chunk 503 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 318 optimal weight: 0.2980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 208 HIS G 241 GLN M 140 HIS ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 GLN R 140 HIS R 151 ASN R 208 HIS U 19 HIS U 208 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 50243 Z= 0.273 Angle : 0.565 12.773 68883 Z= 0.299 Chirality : 0.041 0.197 7511 Planarity : 0.004 0.053 8618 Dihedral : 16.856 178.439 9175 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.85 % Allowed : 19.86 % Favored : 77.29 % 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: -0.28 (0.11), residues: 6156 helix: 1.54 (0.12), residues: 1975 sheet: 0.33 (0.15), residues: 1074 loop : -1.60 (0.11), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 147 HIS 0.004 0.001 HIS A 203 PHE 0.014 0.001 PHE L 152 TYR 0.023 0.002 TYR Q 114 ARG 0.012 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 258 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8593 (m) cc_final: 0.8309 (p) REVERT: B 284 PHE cc_start: 0.7812 (m-80) cc_final: 0.7606 (m-80) REVERT: C 223 GLN cc_start: 0.6310 (mp10) cc_final: 0.5296 (mt0) REVERT: C 285 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7045 (m-10) REVERT: C 301 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8055 (ttmm) REVERT: D 68 ASP cc_start: 0.8004 (m-30) cc_final: 0.7377 (m-30) REVERT: H 34 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7593 (p0) REVERT: H 314 ARG cc_start: 0.8319 (mmt90) cc_final: 0.7793 (mpp80) REVERT: I 21 MET cc_start: 0.3219 (ptt) cc_final: 0.2050 (tpp) REVERT: L 171 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8210 (ptpt) REVERT: L 290 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8794 (pp) REVERT: L 311 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7788 (mtmm) REVERT: M 264 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8230 (tm) REVERT: R 314 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.7072 (mpp80) REVERT: U 127 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: V 46 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: V 209 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8719 (mmmm) REVERT: A 207 ARG cc_start: 0.8243 (ptp-110) cc_final: 0.7877 (ptm-80) REVERT: A 241 GLN cc_start: 0.8147 (tt0) cc_final: 0.7862 (tt0) REVERT: X 59 ARG cc_start: 0.6674 (mtt180) cc_final: 0.5937 (mmt180) REVERT: X 224 ARG cc_start: 0.8256 (mmt-90) cc_final: 0.8043 (tpp-160) outliers start: 123 outliers final: 68 residues processed: 369 average time/residue: 1.2625 time to fit residues: 588.2003 Evaluate side-chains 314 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 239 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 140 HIS Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 77 GLN Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 83 ASP Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 584 optimal weight: 50.0000 chunk 68 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 chunk 343 optimal weight: 0.7980 chunk 510 optimal weight: 2.9990 chunk 338 optimal weight: 4.9990 chunk 604 optimal weight: 0.6980 chunk 378 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS U 208 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 50243 Z= 0.226 Angle : 0.554 15.070 68883 Z= 0.292 Chirality : 0.040 0.223 7511 Planarity : 0.004 0.051 8618 Dihedral : 16.808 178.100 9175 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.64 % Allowed : 20.27 % Favored : 77.08 % 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: -0.12 (0.11), residues: 6156 helix: 1.70 (0.12), residues: 1981 sheet: 0.33 (0.15), residues: 1098 loop : -1.50 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 174 HIS 0.008 0.001 HIS M 140 PHE 0.014 0.001 PHE L 152 TYR 0.024 0.002 TYR Q 114 ARG 0.009 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 260 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8525 (m) cc_final: 0.8270 (p) REVERT: C 223 GLN cc_start: 0.6326 (mp10) cc_final: 0.5399 (mt0) REVERT: C 285 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7170 (m-10) REVERT: C 301 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8036 (ttmm) REVERT: E 283 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: H 34 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7632 (p0) REVERT: H 314 ARG cc_start: 0.8309 (mmt90) cc_final: 0.7831 (mpp80) REVERT: I 21 MET cc_start: 0.3255 (ptt) cc_final: 0.2105 (tpp) REVERT: L 171 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8228 (ptpt) REVERT: L 174 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7453 (ttp-170) REVERT: L 290 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8773 (pp) REVERT: L 311 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7763 (mtmm) REVERT: M 264 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8248 (tm) REVERT: U 127 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: V 46 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: V 190 MET cc_start: 0.8114 (mtm) cc_final: 0.7873 (ptp) REVERT: V 209 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8682 (mmmm) REVERT: A 207 ARG cc_start: 0.8239 (ptp-110) cc_final: 0.7844 (ptm-80) REVERT: A 225 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: A 241 GLN cc_start: 0.8129 (tt0) cc_final: 0.7850 (tt0) REVERT: X 59 ARG cc_start: 0.6592 (mtt180) cc_final: 0.5894 (mmt180) outliers start: 114 outliers final: 68 residues processed: 358 average time/residue: 1.2558 time to fit residues: 566.5087 Evaluate side-chains 315 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 237 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 174 ARG Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 140 HIS Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain X residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 373 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 475 optimal weight: 30.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN I 93 HIS ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS U 208 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 50243 Z= 0.281 Angle : 0.573 12.721 68883 Z= 0.301 Chirality : 0.041 0.214 7511 Planarity : 0.004 0.052 8618 Dihedral : 16.784 178.338 9175 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.46 % Allowed : 20.74 % Favored : 76.80 % 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: -0.07 (0.11), residues: 6156 helix: 1.75 (0.12), residues: 1976 sheet: 0.37 (0.15), residues: 1096 loop : -1.47 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 147 HIS 0.017 0.001 HIS M 140 PHE 0.013 0.001 PHE L 152 TYR 0.026 0.002 TYR Q 114 ARG 0.012 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 254 time to evaluate : 3.931 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: B 177 THR cc_start: 0.8497 (m) cc_final: 0.8216 (p) REVERT: C 223 GLN cc_start: 0.6384 (mp10) cc_final: 0.5463 (mt0) REVERT: C 285 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: C 301 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8068 (ttmm) REVERT: H 34 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7660 (p0) REVERT: H 314 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7840 (mpp80) REVERT: I 21 MET cc_start: 0.3306 (ptt) cc_final: 0.2230 (tpp) REVERT: L 171 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8210 (ptpt) REVERT: L 290 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8771 (pp) REVERT: L 311 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7793 (mtmm) REVERT: M 264 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8256 (tm) REVERT: O 91 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8995 (tp) REVERT: R 314 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.7000 (mpp80) REVERT: S 40 ILE cc_start: 0.1850 (OUTLIER) cc_final: 0.1458 (tp) REVERT: U 127 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: V 46 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: V 190 MET cc_start: 0.8158 (mtm) cc_final: 0.7876 (ptp) REVERT: V 209 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8702 (mmmm) REVERT: A 65 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 66 VAL cc_start: 0.6063 (OUTLIER) cc_final: 0.5652 (m) REVERT: A 81 ASN cc_start: 0.7562 (p0) cc_final: 0.6816 (p0) REVERT: A 207 ARG cc_start: 0.8247 (ptp-110) cc_final: 0.7854 (ptm-80) REVERT: A 241 GLN cc_start: 0.8170 (tt0) cc_final: 0.7899 (tt0) REVERT: X 59 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6054 (mmt180) outliers start: 106 outliers final: 71 residues processed: 348 average time/residue: 1.2824 time to fit residues: 561.1940 Evaluate side-chains 324 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 242 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain X residue 246 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 549 optimal weight: 8.9990 chunk 578 optimal weight: 0.3980 chunk 528 optimal weight: 5.9990 chunk 563 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 442 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 508 optimal weight: 0.9980 chunk 532 optimal weight: 40.0000 chunk 561 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN R 140 HIS U 208 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50243 Z= 0.182 Angle : 0.542 14.436 68883 Z= 0.284 Chirality : 0.040 0.221 7511 Planarity : 0.003 0.050 8618 Dihedral : 16.683 178.723 9175 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.93 % Allowed : 21.27 % Favored : 76.80 % 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: 0.07 (0.11), residues: 6156 helix: 1.86 (0.12), residues: 1993 sheet: 0.45 (0.15), residues: 1103 loop : -1.42 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 147 HIS 0.007 0.001 HIS M 140 PHE 0.017 0.001 PHE I 44 TYR 0.025 0.001 TYR Q 114 ARG 0.015 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8502 (m) cc_final: 0.8218 (p) REVERT: C 221 ASP cc_start: 0.8140 (m-30) cc_final: 0.7754 (t0) REVERT: C 223 GLN cc_start: 0.6322 (mp10) cc_final: 0.5508 (mt0) REVERT: C 301 LYS cc_start: 0.8447 (mmtm) cc_final: 0.7967 (ttmm) REVERT: H 34 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7600 (p0) REVERT: H 125 TYR cc_start: 0.7566 (t80) cc_final: 0.6293 (t80) REVERT: H 314 ARG cc_start: 0.8295 (mmt90) cc_final: 0.7843 (mpp80) REVERT: I 21 MET cc_start: 0.3555 (ptt) cc_final: 0.2202 (tpp) REVERT: L 171 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8206 (ptpt) REVERT: L 290 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8744 (pp) REVERT: M 221 ASP cc_start: 0.7712 (t0) cc_final: 0.7481 (t70) REVERT: M 264 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8250 (tm) REVERT: O 91 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8953 (tp) REVERT: Q 80 ASP cc_start: 0.7957 (m-30) cc_final: 0.7684 (t0) REVERT: R 314 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.7107 (mpp80) REVERT: S 60 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7259 (tp) REVERT: U 127 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7276 (pt0) REVERT: U 190 MET cc_start: 0.8463 (mtp) cc_final: 0.8166 (mtp) REVERT: V 46 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: V 190 MET cc_start: 0.8064 (mtm) cc_final: 0.7859 (ptp) REVERT: V 209 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8643 (mmmm) REVERT: A 65 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 66 VAL cc_start: 0.6120 (OUTLIER) cc_final: 0.5756 (m) REVERT: A 81 ASN cc_start: 0.7619 (p0) cc_final: 0.6841 (p0) REVERT: A 207 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7874 (ptm-80) REVERT: A 208 GLU cc_start: 0.8246 (tp30) cc_final: 0.7869 (tp30) REVERT: A 241 GLN cc_start: 0.8163 (tt0) cc_final: 0.7888 (tt0) REVERT: X 59 ARG cc_start: 0.6690 (mtt180) cc_final: 0.5851 (mmt180) outliers start: 83 outliers final: 56 residues processed: 340 average time/residue: 1.3410 time to fit residues: 569.5115 Evaluate side-chains 308 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 242 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 120 GLN Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 34 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 285 TYR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 144 VAL Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 369 optimal weight: 0.7980 chunk 595 optimal weight: 50.0000 chunk 363 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 624 optimal weight: 50.0000 chunk 574 optimal weight: 30.0000 chunk 497 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 384 optimal weight: 4.9990 chunk 305 optimal weight: 0.0050 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN Q 120 GLN R 140 HIS ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50243 Z= 0.179 Angle : 0.551 20.901 68883 Z= 0.285 Chirality : 0.040 0.278 7511 Planarity : 0.004 0.064 8618 Dihedral : 16.626 179.126 9175 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.58 % Allowed : 21.78 % Favored : 76.64 % 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: 0.16 (0.11), residues: 6156 helix: 1.95 (0.12), residues: 1994 sheet: 0.43 (0.15), residues: 1126 loop : -1.35 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 147 HIS 0.005 0.001 HIS B 196 PHE 0.015 0.001 PHE I 44 TYR 0.025 0.001 TYR Q 114 ARG 0.013 0.000 ARG X 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12312 Ramachandran restraints generated. 6156 Oldfield, 0 Emsley, 6156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 THR cc_start: 0.8499 (m) cc_final: 0.8191 (p) REVERT: C 221 ASP cc_start: 0.8118 (m-30) cc_final: 0.7729 (t0) REVERT: C 223 GLN cc_start: 0.6363 (mp10) cc_final: 0.5548 (mt0) REVERT: C 301 LYS cc_start: 0.8394 (mmtm) cc_final: 0.7900 (ttmm) REVERT: G 58 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7997 (tppp) REVERT: H 34 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7627 (p0) REVERT: H 125 TYR cc_start: 0.7479 (t80) cc_final: 0.6168 (t80) REVERT: H 314 ARG cc_start: 0.8316 (mmt90) cc_final: 0.7831 (mpp80) REVERT: I 21 MET cc_start: 0.3567 (ptt) cc_final: 0.2205 (tpp) REVERT: L 171 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8222 (ptpt) REVERT: L 290 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8734 (pp) REVERT: M 221 ASP cc_start: 0.7717 (t0) cc_final: 0.7486 (t70) REVERT: M 264 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8247 (tm) REVERT: M 301 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8252 (mmtp) REVERT: O 91 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8937 (tp) REVERT: Q 80 ASP cc_start: 0.7961 (m-30) cc_final: 0.7684 (t0) REVERT: R 314 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7182 (mpp80) REVERT: S 60 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7293 (tp) REVERT: U 127 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: U 190 MET cc_start: 0.8446 (mtp) cc_final: 0.8145 (mtp) REVERT: V 46 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: V 190 MET cc_start: 0.8106 (mtm) cc_final: 0.7849 (ptp) REVERT: V 209 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8643 (mmmm) REVERT: A 66 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.6073 (m) REVERT: A 81 ASN cc_start: 0.7605 (p0) cc_final: 0.6803 (p0) REVERT: A 207 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7881 (ptm-80) REVERT: A 208 GLU cc_start: 0.8208 (tp30) cc_final: 0.7905 (tp30) REVERT: A 241 GLN cc_start: 0.8172 (tt0) cc_final: 0.7825 (tt0) REVERT: X 59 ARG cc_start: 0.6651 (mtt180) cc_final: 0.5795 (mmt180) REVERT: X 78 ARG cc_start: 0.6618 (ttp-170) cc_final: 0.6090 (mtt-85) outliers start: 68 outliers final: 49 residues processed: 323 average time/residue: 1.2868 time to fit residues: 520.3631 Evaluate side-chains 304 residues out of total 5025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain L residue 4 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 290 LEU Chi-restraints excluded: chain M residue 140 HIS Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 285 TYR Chi-restraints excluded: chain N residue 50 ARG Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 245 THR Chi-restraints excluded: chain N residue 285 TYR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 285 TYR Chi-restraints excluded: chain P residue 118 LEU Chi-restraints excluded: chain P residue 208 HIS Chi-restraints excluded: chain P residue 285 TYR Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 285 TYR Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 46 TYR Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 209 LYS Chi-restraints excluded: chain A residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 627 random chunks: chunk 395 optimal weight: 0.3980 chunk 529 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 458 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 498 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 511 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 HIS Q 120 GLN ** R 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 208 GLN ** V 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.131311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086033 restraints weight = 115551.726| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.10 r_work: 0.2988 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50243 Z= 0.292 Angle : 0.587 13.291 68883 Z= 0.306 Chirality : 0.041 0.299 7511 Planarity : 0.004 0.048 8618 Dihedral : 16.639 178.372 9173 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.79 % Allowed : 21.85 % Favored : 76.36 % 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: 0.13 (0.11), residues: 6156 helix: 1.89 (0.12), residues: 1990 sheet: 0.49 (0.15), residues: 1094 loop : -1.35 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 174 HIS 0.005 0.001 HIS G 256 PHE 0.013 0.001 PHE C 95 TYR 0.025 0.002 TYR Q 114 ARG 0.014 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10636.41 seconds wall clock time: 186 minutes 30.69 seconds (11190.69 seconds total)