Starting phenix.real_space_refine on Sun Sep 29 17:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8y_3602/09_2024/5n8y_3602.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8y_3602/09_2024/5n8y_3602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8y_3602/09_2024/5n8y_3602.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8y_3602/09_2024/5n8y_3602.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8y_3602/09_2024/5n8y_3602.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8y_3602/09_2024/5n8y_3602.cif" } resolution = 4.7 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= 0.004 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: 3 Type Number sf(0) Gaussians C 14010 2.51 5 N 4752 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23514 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2381 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 12, 'TRANS': 470} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1900 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 12, 'ASN:plan1': 17, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 28, 'GLU:plan': 37, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 850 Chain: "B" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2381 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 12, 'TRANS': 470} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1900 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 12, 'ASN:plan1': 17, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 28, 'GLU:plan': 37, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 850 Chain: "C" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2381 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 12, 'TRANS': 470} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1900 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 12, 'ASN:plan1': 17, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 28, 'GLU:plan': 37, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 850 Chain: "D" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2381 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 12, 'TRANS': 470} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1900 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 12, 'ASN:plan1': 17, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 28, 'GLU:plan': 37, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 850 Chain: "E" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2381 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 12, 'TRANS': 470} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1900 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 12, 'ASN:plan1': 17, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 28, 'GLU:plan': 37, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 850 Chain: "F" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 2381 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 12, 'TRANS': 470} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1492 Unresolved non-hydrogen angles: 1900 Unresolved non-hydrogen dihedrals: 1225 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 8, 'TYR:plan': 12, 'ASN:plan1': 17, 'TRP:plan': 3, 'ASP:plan': 26, 'PHE:plan': 28, 'GLU:plan': 37, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 850 Chain: "G" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "H" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "K" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "J" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "I" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "L" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 221 Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 221 Chain: "P" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 221 Chain: "R" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 221 Chain: "T" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 221 Chain: "V" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "W" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 216 Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 544 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 378 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 221 Time building chain proxies: 14.49, per 1000 atoms: 0.62 Number of scatterers: 23514 At special positions: 0 Unit cell: (182.25, 174.15, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4752 8.00 N 4752 7.00 C 14010 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: 6.80 Conformation dependent library (CDL) restraints added in 4.2 seconds 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8940 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 30 sheets defined 52.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.588A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.529A pdb=" N ARG A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.630A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.602A pdb=" N VAL A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 192 through 199 removed outlier: 3.574A pdb=" N VAL A 196 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 293 through 308 removed outlier: 3.872A pdb=" N VAL A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.910A pdb=" N SER A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 355 through 371 removed outlier: 3.663A pdb=" N HIS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.543A pdb=" N GLY A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 51 through 68 removed outlier: 3.589A pdb=" N LEU B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 88 removed outlier: 3.529A pdb=" N ARG B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.630A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.602A pdb=" N VAL B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 192 through 199 removed outlier: 3.573A pdb=" N VAL B 196 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 293 through 308 removed outlier: 3.872A pdb=" N VAL B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 332 removed outlier: 3.910A pdb=" N SER B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 355 through 371 removed outlier: 3.663A pdb=" N HIS B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.543A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.588A pdb=" N LEU C 60 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.530A pdb=" N ARG C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.631A pdb=" N LEU C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 137 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.602A pdb=" N VAL C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.573A pdb=" N VAL C 196 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 293 through 308 removed outlier: 3.871A pdb=" N VAL C 298 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS C 306 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 332 removed outlier: 3.910A pdb=" N SER C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 355 through 371 removed outlier: 3.664A pdb=" N HIS C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 388 through 406 removed outlier: 3.544A pdb=" N GLY C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 402 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.588A pdb=" N LEU D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 removed outlier: 3.529A pdb=" N ARG D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.630A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.602A pdb=" N VAL D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 175 Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.574A pdb=" N VAL D 196 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 293 through 308 removed outlier: 3.873A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 332 removed outlier: 3.909A pdb=" N SER D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 355 through 371 removed outlier: 3.663A pdb=" N HIS D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 388 through 406 removed outlier: 3.543A pdb=" N GLY D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 402 " --> pdb=" O GLY D 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.588A pdb=" N LEU E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 88 removed outlier: 3.529A pdb=" N ARG E 88 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 93 through 100 removed outlier: 3.631A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 137 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.601A pdb=" N VAL E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E 154 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 192 through 199 removed outlier: 3.573A pdb=" N VAL E 196 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU E 197 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 293 through 308 removed outlier: 3.872A pdb=" N VAL E 298 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER E 299 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN E 304 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA E 305 " --> pdb=" O PHE E 301 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS E 306 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA E 307 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 332 removed outlier: 3.909A pdb=" N SER E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 341 Processing helix chain 'E' and resid 355 through 371 removed outlier: 3.663A pdb=" N HIS E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.543A pdb=" N GLY E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 402 " --> pdb=" O GLY E 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 51 through 68 removed outlier: 3.589A pdb=" N LEU F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 88 removed outlier: 3.529A pdb=" N ARG F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 93 through 100 removed outlier: 3.630A pdb=" N LEU F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 137 Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.602A pdb=" N VAL F 150 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 Processing helix chain 'F' and resid 192 through 199 removed outlier: 3.574A pdb=" N VAL F 196 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU F 197 " --> pdb=" O TYR F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 293 through 308 removed outlier: 3.872A pdb=" N VAL F 298 " --> pdb=" O LYS F 294 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER F 299 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA F 305 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS F 306 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 332 removed outlier: 3.910A pdb=" N SER F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 341 Processing helix chain 'F' and resid 355 through 371 removed outlier: 3.664A pdb=" N HIS F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.543A pdb=" N GLY F 401 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR F 402 " --> pdb=" O GLY F 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 34 removed outlier: 3.648A pdb=" N GLU G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 removed outlier: 4.075A pdb=" N ALA G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 98 Processing helix chain 'H' and resid 17 through 34 removed outlier: 3.649A pdb=" N GLU H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 56 removed outlier: 4.074A pdb=" N ALA H 53 " --> pdb=" O ASN H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 98 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.649A pdb=" N GLU K 34 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 56 removed outlier: 4.074A pdb=" N ALA K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 98 Processing helix chain 'J' and resid 17 through 34 removed outlier: 3.649A pdb=" N GLU J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 56 removed outlier: 4.074A pdb=" N ALA J 53 " --> pdb=" O ASN J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 98 Processing helix chain 'I' and resid 17 through 34 removed outlier: 3.648A pdb=" N GLU I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 56 removed outlier: 4.074A pdb=" N ALA I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 98 Processing helix chain 'L' and resid 17 through 34 removed outlier: 3.649A pdb=" N GLU L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 removed outlier: 4.075A pdb=" N ALA L 53 " --> pdb=" O ASN L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 98 Processing helix chain 'M' and resid 183 through 206 removed outlier: 4.674A pdb=" N PHE M 206 " --> pdb=" O VAL M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 226 Processing helix chain 'M' and resid 229 through 250 removed outlier: 3.653A pdb=" N VAL M 233 " --> pdb=" O PRO M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 261 through 280 removed outlier: 3.739A pdb=" N ASP M 267 " --> pdb=" O LEU M 263 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL M 268 " --> pdb=" O THR M 264 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE M 269 " --> pdb=" O LEU M 265 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA M 270 " --> pdb=" O ILE M 266 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE M 280 " --> pdb=" O TYR M 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 182 removed outlier: 6.277A pdb=" N LEU N 179 " --> pdb=" O ASP N 176 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG N 180 " --> pdb=" O ARG N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 206 removed outlier: 4.732A pdb=" N PHE N 206 " --> pdb=" O VAL N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 226 Processing helix chain 'N' and resid 229 through 251 removed outlier: 3.751A pdb=" N VAL N 233 " --> pdb=" O PRO N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 260 removed outlier: 3.755A pdb=" N ILE N 257 " --> pdb=" O SER N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 279 Processing helix chain 'O' and resid 183 through 206 removed outlier: 4.675A pdb=" N PHE O 206 " --> pdb=" O VAL O 202 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 226 Processing helix chain 'O' and resid 229 through 250 removed outlier: 3.653A pdb=" N VAL O 233 " --> pdb=" O PRO O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 260 Processing helix chain 'O' and resid 261 through 280 removed outlier: 3.739A pdb=" N ASP O 267 " --> pdb=" O LEU O 263 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL O 268 " --> pdb=" O THR O 264 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE O 269 " --> pdb=" O LEU O 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA O 270 " --> pdb=" O ILE O 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE O 280 " --> pdb=" O TYR O 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 182 removed outlier: 6.279A pdb=" N LEU P 179 " --> pdb=" O ASP P 176 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG P 180 " --> pdb=" O ARG P 177 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 206 removed outlier: 4.731A pdb=" N PHE P 206 " --> pdb=" O VAL P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 Processing helix chain 'P' and resid 229 through 251 removed outlier: 3.751A pdb=" N VAL P 233 " --> pdb=" O PRO P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 260 removed outlier: 3.756A pdb=" N ILE P 257 " --> pdb=" O SER P 254 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 279 Processing helix chain 'Q' and resid 183 through 206 removed outlier: 4.674A pdb=" N PHE Q 206 " --> pdb=" O VAL Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 226 Processing helix chain 'Q' and resid 229 through 250 removed outlier: 3.653A pdb=" N VAL Q 233 " --> pdb=" O PRO Q 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 256 through 260 Processing helix chain 'Q' and resid 261 through 280 removed outlier: 3.739A pdb=" N ASP Q 267 " --> pdb=" O LEU Q 263 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL Q 268 " --> pdb=" O THR Q 264 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA Q 270 " --> pdb=" O ILE Q 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE Q 280 " --> pdb=" O TYR Q 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 182 removed outlier: 6.279A pdb=" N LEU R 179 " --> pdb=" O ASP R 176 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG R 180 " --> pdb=" O ARG R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 206 removed outlier: 4.733A pdb=" N PHE R 206 " --> pdb=" O VAL R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 226 Processing helix chain 'R' and resid 229 through 251 removed outlier: 3.751A pdb=" N VAL R 233 " --> pdb=" O PRO R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 260 removed outlier: 3.757A pdb=" N ILE R 257 " --> pdb=" O SER R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 279 Processing helix chain 'S' and resid 183 through 206 removed outlier: 4.675A pdb=" N PHE S 206 " --> pdb=" O VAL S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 211 through 226 Processing helix chain 'S' and resid 229 through 250 removed outlier: 3.653A pdb=" N VAL S 233 " --> pdb=" O PRO S 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 256 through 260 Processing helix chain 'S' and resid 261 through 280 removed outlier: 3.740A pdb=" N ASP S 267 " --> pdb=" O LEU S 263 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL S 268 " --> pdb=" O THR S 264 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE S 269 " --> pdb=" O LEU S 265 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA S 270 " --> pdb=" O ILE S 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE S 280 " --> pdb=" O TYR S 276 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 182 removed outlier: 6.278A pdb=" N LEU T 179 " --> pdb=" O ASP T 176 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG T 180 " --> pdb=" O ARG T 177 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 206 removed outlier: 4.732A pdb=" N PHE T 206 " --> pdb=" O VAL T 202 " (cutoff:3.500A) Processing helix chain 'T' and resid 211 through 226 Processing helix chain 'T' and resid 229 through 251 removed outlier: 3.752A pdb=" N VAL T 233 " --> pdb=" O PRO T 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 254 through 260 removed outlier: 3.757A pdb=" N ILE T 257 " --> pdb=" O SER T 254 " (cutoff:3.500A) Processing helix chain 'T' and resid 261 through 279 Processing helix chain 'U' and resid 183 through 206 removed outlier: 4.675A pdb=" N PHE U 206 " --> pdb=" O VAL U 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 226 Processing helix chain 'U' and resid 229 through 250 removed outlier: 3.652A pdb=" N VAL U 233 " --> pdb=" O PRO U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 260 Processing helix chain 'U' and resid 261 through 280 removed outlier: 3.739A pdb=" N ASP U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL U 268 " --> pdb=" O THR U 264 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE U 269 " --> pdb=" O LEU U 265 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA U 270 " --> pdb=" O ILE U 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE U 280 " --> pdb=" O TYR U 276 " (cutoff:3.500A) Processing helix chain 'V' and resid 174 through 182 removed outlier: 6.277A pdb=" N LEU V 179 " --> pdb=" O ASP V 176 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG V 180 " --> pdb=" O ARG V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 206 removed outlier: 4.733A pdb=" N PHE V 206 " --> pdb=" O VAL V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 211 through 226 Processing helix chain 'V' and resid 229 through 251 removed outlier: 3.751A pdb=" N VAL V 233 " --> pdb=" O PRO V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 254 through 260 removed outlier: 3.755A pdb=" N ILE V 257 " --> pdb=" O SER V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 261 through 279 Processing helix chain 'W' and resid 183 through 206 removed outlier: 4.674A pdb=" N PHE W 206 " --> pdb=" O VAL W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 211 through 226 Processing helix chain 'W' and resid 229 through 250 removed outlier: 3.652A pdb=" N VAL W 233 " --> pdb=" O PRO W 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 256 through 260 Processing helix chain 'W' and resid 261 through 280 removed outlier: 3.738A pdb=" N ASP W 267 " --> pdb=" O LEU W 263 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL W 268 " --> pdb=" O THR W 264 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE W 269 " --> pdb=" O LEU W 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA W 270 " --> pdb=" O ILE W 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE W 280 " --> pdb=" O TYR W 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 182 removed outlier: 6.278A pdb=" N LEU X 179 " --> pdb=" O ASP X 176 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG X 180 " --> pdb=" O ARG X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 206 removed outlier: 4.732A pdb=" N PHE X 206 " --> pdb=" O VAL X 202 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 226 Processing helix chain 'X' and resid 229 through 251 removed outlier: 3.750A pdb=" N VAL X 233 " --> pdb=" O PRO X 229 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 removed outlier: 3.757A pdb=" N ILE X 257 " --> pdb=" O SER X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 261 through 279 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.645A pdb=" N GLY A 71 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 106 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 73 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER A 41 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL A 205 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.742A pdb=" N ILE A 375 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 411 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 286 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 283 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 438 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 285 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 440 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR A 287 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR A 442 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 457 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 439 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL A 455 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN A 441 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE A 453 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 468 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 469 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.644A pdb=" N GLY B 71 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU B 106 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE B 73 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER B 41 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL B 205 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 43 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 207 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER B 45 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN B 209 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA8, first strand: chain 'B' and resid 374 through 376 removed outlier: 3.743A pdb=" N ILE B 375 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 411 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 286 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE B 283 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 438 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 285 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 440 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR B 287 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR B 442 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 457 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 439 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL B 455 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 441 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE B 453 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 468 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 469 " --> pdb=" O LYS B 480 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.645A pdb=" N GLY C 71 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU C 106 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE C 73 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER C 41 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL C 205 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 43 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU C 207 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER C 45 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN C 209 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AB3, first strand: chain 'C' and resid 374 through 376 removed outlier: 3.742A pdb=" N ILE C 375 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 411 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 286 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE C 283 " --> pdb=" O THR C 436 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE C 438 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 285 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU C 440 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 287 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR C 442 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 457 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C 439 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL C 455 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN C 441 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE C 453 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG C 468 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 469 " --> pdb=" O LYS C 480 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.646A pdb=" N GLY D 71 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU D 106 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE D 73 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER D 41 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL D 205 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AB7, first strand: chain 'D' and resid 374 through 376 removed outlier: 3.742A pdb=" N ILE D 375 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 411 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 286 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE D 283 " --> pdb=" O THR D 436 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE D 438 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 285 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 440 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR D 287 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR D 442 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 457 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 439 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL D 455 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 441 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE D 453 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D 468 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 469 " --> pdb=" O LYS D 480 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.645A pdb=" N GLY E 71 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 106 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE E 73 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER E 41 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL E 205 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU E 43 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU E 207 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER E 45 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN E 209 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 262 through 263 Processing sheet with id=AC2, first strand: chain 'E' and resid 374 through 376 removed outlier: 3.742A pdb=" N ILE E 375 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E 411 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 286 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE E 283 " --> pdb=" O THR E 436 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE E 438 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU E 285 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 440 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR E 287 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N TYR E 442 " --> pdb=" O THR E 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 457 " --> pdb=" O ILE E 437 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU E 439 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL E 455 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN E 441 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 453 " --> pdb=" O GLN E 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG E 468 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 469 " --> pdb=" O LYS E 480 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'F' and resid 103 through 107 removed outlier: 6.645A pdb=" N GLY F 71 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU F 106 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE F 73 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER F 41 " --> pdb=" O ASN F 203 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL F 205 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 43 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 207 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER F 45 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN F 209 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 12.878A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 262 through 263 Processing sheet with id=AC6, first strand: chain 'F' and resid 374 through 376 removed outlier: 3.742A pdb=" N ILE F 375 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 411 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 286 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE F 283 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE F 438 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU F 285 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU F 440 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR F 287 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR F 442 " --> pdb=" O THR F 287 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS F 457 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU F 439 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL F 455 " --> pdb=" O LEU F 439 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN F 441 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE F 453 " --> pdb=" O GLN F 441 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG F 468 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU F 469 " --> pdb=" O LYS F 480 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 40 through 45 removed outlier: 6.519A pdb=" N LEU G 9 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE G 44 " --> pdb=" O LEU G 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU G 11 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE G 8 " --> pdb=" O VAL G 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 40 through 45 removed outlier: 6.519A pdb=" N LEU H 9 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE H 44 " --> pdb=" O LEU H 9 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU H 11 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE H 8 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 40 through 45 removed outlier: 6.518A pdb=" N LEU K 9 " --> pdb=" O LYS K 42 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE K 44 " --> pdb=" O LEU K 9 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU K 11 " --> pdb=" O ILE K 44 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE K 8 " --> pdb=" O VAL K 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 40 through 45 removed outlier: 6.519A pdb=" N LEU J 9 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE J 44 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU J 11 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 8 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 40 through 45 removed outlier: 6.519A pdb=" N LEU I 9 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE I 44 " --> pdb=" O LEU I 9 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU I 11 " --> pdb=" O ILE I 44 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE I 8 " --> pdb=" O VAL I 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 40 through 45 removed outlier: 6.518A pdb=" N LEU L 9 " --> pdb=" O LYS L 42 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE L 44 " --> pdb=" O LEU L 9 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU L 11 " --> pdb=" O ILE L 44 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE L 8 " --> pdb=" O VAL L 67 " (cutoff:3.500A) 1902 hydrogen bonds defined for protein. 5364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.29 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.24: 4489 1.24 - 1.41: 4979 1.41 - 1.57: 13967 1.57 - 1.73: 43 1.73 - 1.90: 12 Bond restraints: 23490 Sorted by residual: bond pdb=" C ARG M 177 " pdb=" N PHE M 178 " ideal model delta sigma weight residual 1.332 1.898 -0.566 1.40e-02 5.10e+03 1.63e+03 bond pdb=" C ARG Q 177 " pdb=" N PHE Q 178 " ideal model delta sigma weight residual 1.332 1.898 -0.566 1.40e-02 5.10e+03 1.63e+03 bond pdb=" C ARG O 177 " pdb=" N PHE O 178 " ideal model delta sigma weight residual 1.332 1.898 -0.566 1.40e-02 5.10e+03 1.63e+03 bond pdb=" C ARG U 177 " pdb=" N PHE U 178 " ideal model delta sigma weight residual 1.332 1.897 -0.565 1.40e-02 5.10e+03 1.63e+03 bond pdb=" C ARG W 177 " pdb=" N PHE W 178 " ideal model delta sigma weight residual 1.332 1.897 -0.565 1.40e-02 5.10e+03 1.63e+03 ... (remaining 23485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.03: 32610 17.03 - 34.05: 30 34.05 - 51.08: 24 51.08 - 68.10: 6 68.10 - 85.13: 6 Bond angle restraints: 32676 Sorted by residual: angle pdb=" O ARG M 177 " pdb=" C ARG M 177 " pdb=" N PHE M 178 " ideal model delta sigma weight residual 122.84 37.71 85.13 1.16e+00 7.43e-01 5.39e+03 angle pdb=" O ARG W 177 " pdb=" C ARG W 177 " pdb=" N PHE W 178 " ideal model delta sigma weight residual 122.84 37.71 85.13 1.16e+00 7.43e-01 5.39e+03 angle pdb=" O ARG O 177 " pdb=" C ARG O 177 " pdb=" N PHE O 178 " ideal model delta sigma weight residual 122.84 37.72 85.12 1.16e+00 7.43e-01 5.38e+03 angle pdb=" O ARG S 177 " pdb=" C ARG S 177 " pdb=" N PHE S 178 " ideal model delta sigma weight residual 122.84 37.72 85.12 1.16e+00 7.43e-01 5.38e+03 angle pdb=" O ARG Q 177 " pdb=" C ARG Q 177 " pdb=" N PHE Q 178 " ideal model delta sigma weight residual 122.84 37.72 85.12 1.16e+00 7.43e-01 5.38e+03 ... (remaining 32671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 13486 14.57 - 29.15: 176 29.15 - 43.72: 18 43.72 - 58.30: 6 58.30 - 72.87: 6 Dihedral angle restraints: 13692 sinusoidal: 24 harmonic: 13668 Sorted by residual: dihedral pdb=" CA THR I 6 " pdb=" C THR I 6 " pdb=" N TYR I 7 " pdb=" CA TYR I 7 " ideal model delta harmonic sigma weight residual 180.00 107.13 72.87 0 5.00e+00 4.00e-02 2.12e+02 dihedral pdb=" CA THR H 6 " pdb=" C THR H 6 " pdb=" N TYR H 7 " pdb=" CA TYR H 7 " ideal model delta harmonic sigma weight residual 180.00 107.26 72.74 0 5.00e+00 4.00e-02 2.12e+02 dihedral pdb=" CA THR K 6 " pdb=" C THR K 6 " pdb=" N TYR K 7 " pdb=" CA TYR K 7 " ideal model delta harmonic sigma weight residual 180.00 107.26 72.74 0 5.00e+00 4.00e-02 2.12e+02 ... (remaining 13689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3445 0.082 - 0.165: 788 0.165 - 0.247: 178 0.247 - 0.330: 47 0.330 - 0.412: 24 Chirality restraints: 4482 Sorted by residual: chirality pdb=" CA GLU Q 235 " pdb=" N GLU Q 235 " pdb=" C GLU Q 235 " pdb=" CB GLU Q 235 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA GLU O 235 " pdb=" N GLU O 235 " pdb=" C GLU O 235 " pdb=" CB GLU O 235 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA GLU U 235 " pdb=" N GLU U 235 " pdb=" C GLU U 235 " pdb=" CB GLU U 235 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 4479 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 122 " 0.049 2.00e-02 2.50e+03 1.83e-01 3.34e+02 pdb=" C ASP B 122 " -0.310 2.00e-02 2.50e+03 pdb=" O ASP B 122 " 0.150 2.00e-02 2.50e+03 pdb=" N LEU B 123 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 122 " 0.049 2.00e-02 2.50e+03 1.83e-01 3.34e+02 pdb=" C ASP E 122 " -0.310 2.00e-02 2.50e+03 pdb=" O ASP E 122 " 0.150 2.00e-02 2.50e+03 pdb=" N LEU E 123 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 122 " 0.049 2.00e-02 2.50e+03 1.83e-01 3.33e+02 pdb=" C ASP A 122 " -0.310 2.00e-02 2.50e+03 pdb=" O ASP A 122 " 0.150 2.00e-02 2.50e+03 pdb=" N LEU A 123 " 0.111 2.00e-02 2.50e+03 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 28 1.61 - 2.43: 270 2.43 - 3.26: 27019 3.26 - 4.08: 50113 4.08 - 4.90: 81141 Warning: very small nonbonded interaction distances. Nonbonded interactions: 158571 Sorted by model distance: nonbonded pdb=" CA VAL E 118 " pdb=" C LEU K 79 " model vdw 0.788 3.700 nonbonded pdb=" O ARG W 177 " pdb=" CA PHE W 178 " model vdw 0.992 2.776 nonbonded pdb=" O ARG M 177 " pdb=" CA PHE M 178 " model vdw 0.992 2.776 nonbonded pdb=" O ARG S 177 " pdb=" CA PHE S 178 " model vdw 0.992 2.776 nonbonded pdb=" O ARG U 177 " pdb=" CA PHE U 178 " model vdw 0.993 2.776 ... (remaining 158566 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 174 through 280) selection = chain 'N' selection = (chain 'O' and resid 174 through 280) selection = chain 'P' selection = (chain 'Q' and resid 174 through 280) selection = chain 'R' selection = (chain 'S' and resid 174 through 280) selection = chain 'T' selection = (chain 'U' and resid 174 through 280) selection = chain 'V' selection = chain 'W' selection = (chain 'X' and resid 174 through 280) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 56.600 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 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 : 0.017 0.566 23490 Z= 1.243 Angle : 2.387 85.129 32676 Z= 1.777 Chirality : 0.081 0.412 4482 Planarity : 0.010 0.183 4728 Dihedral : 7.588 72.870 4752 Min Nonbonded Distance : 0.788 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 1.38 % Allowed : 4.23 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.65 (0.11), residues: 4704 helix: -0.58 (0.10), residues: 2070 sheet: -0.37 (0.17), residues: 762 loop : -1.91 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 3.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2036 time to fit residues: 58.3899 Evaluate side-chains 144 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 20.0000 chunk 350 optimal weight: 40.0000 chunk 194 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 362 optimal weight: 20.0000 chunk 140 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 chunk 269 optimal weight: 40.0000 chunk 419 optimal weight: 30.0000 overall best weight: 13.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 23490 Z= 0.471 Angle : 0.938 18.594 32676 Z= 0.598 Chirality : 0.048 0.205 4482 Planarity : 0.007 0.042 4728 Dihedral : 8.185 37.318 4728 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.46 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.42 % 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: -2.25 (0.11), residues: 4704 helix: -0.62 (0.10), residues: 2160 sheet: -1.26 (0.17), residues: 796 loop : -2.63 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.624 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2007 time to fit residues: 55.5009 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 349 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 420 optimal weight: 0.0070 chunk 454 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 143 optimal weight: 0.0570 chunk 337 optimal weight: 8.9990 overall best weight: 3.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 23490 Z= 0.152 Angle : 0.508 8.298 32676 Z= 0.310 Chirality : 0.043 0.154 4482 Planarity : 0.002 0.018 4728 Dihedral : 5.170 34.246 4728 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.12), residues: 4704 helix: 1.21 (0.11), residues: 2291 sheet: -1.30 (0.17), residues: 852 loop : -2.26 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2171 time to fit residues: 60.3558 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 40.0000 chunk 316 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 200 optimal weight: 7.9990 chunk 282 optimal weight: 20.0000 chunk 421 optimal weight: 5.9990 chunk 446 optimal weight: 30.0000 chunk 220 optimal weight: 20.0000 chunk 399 optimal weight: 40.0000 chunk 120 optimal weight: 30.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 1.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23490 Z= 0.369 Angle : 0.756 9.842 32676 Z= 0.481 Chirality : 0.045 0.156 4482 Planarity : 0.005 0.023 4728 Dihedral : 7.470 34.636 4728 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.86 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.07 (0.11), residues: 4704 helix: -0.01 (0.10), residues: 2175 sheet: -1.85 (0.18), residues: 782 loop : -2.87 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.771 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2109 time to fit residues: 58.4530 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 332 optimal weight: 20.0000 chunk 184 optimal weight: 3.9990 chunk 381 optimal weight: 30.0000 chunk 308 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 400 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 1.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 23490 Z= 0.202 Angle : 0.547 9.578 32676 Z= 0.339 Chirality : 0.043 0.154 4482 Planarity : 0.003 0.015 4728 Dihedral : 5.776 29.536 4728 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.50 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.23 (0.12), residues: 4704 helix: 0.88 (0.11), residues: 2253 sheet: -1.88 (0.17), residues: 832 loop : -2.66 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.498 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2075 time to fit residues: 57.2550 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 1.9990 chunk 402 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 447 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 1.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 23490 Z= 0.177 Angle : 0.495 7.264 32676 Z= 0.307 Chirality : 0.042 0.146 4482 Planarity : 0.002 0.012 4728 Dihedral : 5.027 42.349 4728 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.80 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4704 helix: 1.68 (0.11), residues: 2222 sheet: -1.87 (0.17), residues: 852 loop : -2.43 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.564 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2384 time to fit residues: 67.7692 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 chunk 254 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 376 optimal weight: 30.0000 chunk 249 optimal weight: 0.0020 chunk 445 optimal weight: 30.0000 chunk 278 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 1.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23490 Z= 0.332 Angle : 0.693 9.224 32676 Z= 0.439 Chirality : 0.044 0.158 4482 Planarity : 0.004 0.018 4728 Dihedral : 6.908 57.454 4728 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.56 % Favored : 86.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.96 (0.12), residues: 4704 helix: 0.38 (0.11), residues: 2188 sheet: -2.37 (0.17), residues: 798 loop : -2.97 (0.13), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.565 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2078 time to fit residues: 57.8031 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 265 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 283 optimal weight: 30.0000 chunk 303 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 1.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 23490 Z= 0.191 Angle : 0.525 8.047 32676 Z= 0.325 Chirality : 0.042 0.166 4482 Planarity : 0.002 0.014 4728 Dihedral : 5.559 47.955 4728 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.71 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.12), residues: 4704 helix: 1.06 (0.11), residues: 2256 sheet: -2.33 (0.17), residues: 816 loop : -2.88 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.705 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2267 time to fit residues: 63.3838 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 0.0570 chunk 426 optimal weight: 30.0000 chunk 389 optimal weight: 40.0000 chunk 414 optimal weight: 30.0000 chunk 249 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 325 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 chunk 392 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 overall best weight: 5.9308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 1.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 23490 Z= 0.210 Angle : 0.540 7.611 32676 Z= 0.336 Chirality : 0.043 0.197 4482 Planarity : 0.003 0.014 4728 Dihedral : 5.641 48.127 4728 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.90 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4704 helix: 1.08 (0.11), residues: 2259 sheet: -2.34 (0.17), residues: 816 loop : -2.87 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2020 time to fit residues: 55.9407 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 30.0000 chunk 438 optimal weight: 30.0000 chunk 267 optimal weight: 40.0000 chunk 208 optimal weight: 20.0000 chunk 305 optimal weight: 20.0000 chunk 460 optimal weight: 30.0000 chunk 423 optimal weight: 9.9990 chunk 366 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 224 optimal weight: 30.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 1.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 23490 Z= 0.573 Angle : 0.953 14.254 32676 Z= 0.617 Chirality : 0.048 0.173 4482 Planarity : 0.006 0.027 4728 Dihedral : 8.416 58.543 4728 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.94 % Favored : 82.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.64 (0.11), residues: 4704 helix: -1.16 (0.10), residues: 2178 sheet: -2.85 (0.18), residues: 726 loop : -3.76 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.746 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2103 time to fit residues: 58.3853 Evaluate side-chains 138 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 0.9990 chunk 390 optimal weight: 50.0000 chunk 112 optimal weight: 20.0000 chunk 337 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 367 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107429 restraints weight = 107316.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 110)---------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106602 restraints weight = 137195.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106082 restraints weight = 138129.502| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 1.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23490 Z= 0.208 Angle : 0.555 7.989 32676 Z= 0.346 Chirality : 0.043 0.174 4482 Planarity : 0.003 0.019 4728 Dihedral : 6.055 41.535 4728 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.97 % Favored : 88.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.27 (0.12), residues: 4704 helix: 0.32 (0.11), residues: 2269 sheet: -2.63 (0.19), residues: 696 loop : -3.55 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 92 PHE 0.000 0.000 PHE A 28 TYR 0.000 0.000 TYR A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2975.92 seconds wall clock time: 53 minutes 20.30 seconds (3200.30 seconds total)