Starting phenix.real_space_refine on Fri Feb 23 22:40:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0w_4699/02_2024/6r0w_4699_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0w_4699/02_2024/6r0w_4699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0w_4699/02_2024/6r0w_4699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0w_4699/02_2024/6r0w_4699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0w_4699/02_2024/6r0w_4699_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0w_4699/02_2024/6r0w_4699_updated.pdb" } resolution = 3.6 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= 0.004 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 103 5.16 5 C 25044 2.51 5 N 7293 2.21 5 O 7736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 410": "NH1" <-> "NH2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 106": "NH1" <-> "NH2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40181 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "E" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3616 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 435} Chain: "F" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3626 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 436} Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1628 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 808 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 15, 'GLU:plan': 26, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 566 Chain: "N" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 3190 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2030 Unresolved non-hydrogen angles: 2628 Unresolved non-hydrogen dihedrals: 1714 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 12, 'TYR:plan': 18, 'ASN:plan1': 7, 'TRP:plan': 12, 'HIS:plan': 21, 'PHE:plan': 33, 'GLU:plan': 56, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1071 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 356 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 347 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.90, per 1000 atoms: 0.57 Number of scatterers: 40181 At special positions: 0 Unit cell: (149.73, 148.645, 257.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 4 15.00 Mg 1 11.99 O 7736 8.00 N 7293 7.00 C 25044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.47 Conformation dependent library (CDL) restraints added in 9.2 seconds 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 36 sheets defined 52.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.10 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 314 removed outlier: 5.115A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'A' and resid 352 through 362 removed outlier: 4.416A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 358 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 362 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 463 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 481 through 493 Processing helix chain 'A' and resid 509 through 531 removed outlier: 3.706A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 No H-bonds generated for 'chain 'A' and resid 537 through 540' Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.507A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 removed outlier: 3.551A pdb=" N ARG B 284 " --> pdb=" O LEU B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 298 through 315 removed outlier: 4.467A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.024A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 447 through 470 removed outlier: 4.307A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 removed outlier: 4.060A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 559 through 575 removed outlier: 3.794A pdb=" N GLU B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.980A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.899A pdb=" N ARG C 299 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 316 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 364 removed outlier: 4.255A pdb=" N ALA C 355 " --> pdb=" O PRO C 352 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU C 363 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 432 through 442 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 470 removed outlier: 4.578A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 539 No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 559 through 575 removed outlier: 4.713A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.645A pdb=" N ARG D 216 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.763A pdb=" N ALA D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.231A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 291 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 293 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 3.862A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 344 No H-bonds generated for 'chain 'D' and resid 341 through 344' Processing helix chain 'D' and resid 375 through 398 removed outlier: 3.970A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.902A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 4.401A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 161 through 170 Processing helix chain 'E' and resid 201 through 211 Processing helix chain 'E' and resid 230 through 247 removed outlier: 3.594A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.673A pdb=" N ALA E 246 " --> pdb=" O GLU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 271 removed outlier: 3.808A pdb=" N ILE E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 Processing helix chain 'E' and resid 324 through 332 Processing helix chain 'E' and resid 341 through 345 removed outlier: 3.515A pdb=" N ARG E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 341 through 345' Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 3.768A pdb=" N LEU E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 409 through 421 removed outlier: 3.688A pdb=" N ASP E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 removed outlier: 4.099A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 460 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 198 through 211 removed outlier: 4.239A pdb=" N GLU F 209 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 248 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.377A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR F 293 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 375 through 399 removed outlier: 4.025A pdb=" N ASP F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE F 392 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 407 through 421 removed outlier: 4.125A pdb=" N ARG F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.167A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'G' and resid 8 through 69 removed outlier: 3.714A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 81 Processing helix chain 'G' and resid 122 through 168 removed outlier: 3.945A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 205 removed outlier: 4.119A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 16 removed outlier: 4.160A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.022A pdb=" N ALA H 58 " --> pdb=" O PRO H 55 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 59 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 62 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 19 through 103 removed outlier: 4.271A pdb=" N GLU I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 117 Processing helix chain 'J' and resid 3 through 94 removed outlier: 4.686A pdb=" N GLU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 114 removed outlier: 4.252A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 131 No H-bonds generated for 'chain 'J' and resid 128 through 131' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.970A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 103 removed outlier: 4.629A pdb=" N GLN K 32 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.921A pdb=" N VAL K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 92 removed outlier: 6.037A pdb=" N GLN L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 113 Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 168 through 186 removed outlier: 5.140A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN L 184 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 17 removed outlier: 3.749A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 removed outlier: 3.625A pdb=" N ALA M 28 " --> pdb=" O PHE M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 42 Processing helix chain 'M' and resid 45 through 48 removed outlier: 3.856A pdb=" N GLU M 48 " --> pdb=" O TYR M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 45 through 48' Processing helix chain 'M' and resid 54 through 73 removed outlier: 4.494A pdb=" N ASP M 71 " --> pdb=" O LYS M 67 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Proline residue: M 73 - end of helix Processing helix chain 'M' and resid 79 through 86 removed outlier: 4.163A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 121 through 128 removed outlier: 3.628A pdb=" N TYR M 128 " --> pdb=" O TRP M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 146 through 154 Processing helix chain 'M' and resid 162 through 181 Processing helix chain 'M' and resid 188 through 206 Processing helix chain 'M' and resid 214 through 217 No H-bonds generated for 'chain 'M' and resid 214 through 217' Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 238 through 242 Processing helix chain 'M' and resid 258 through 278 removed outlier: 4.029A pdb=" N GLY M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 309 Processing helix chain 'M' and resid 317 through 319 No H-bonds generated for 'chain 'M' and resid 317 through 319' Processing helix chain 'N' and resid 14 through 26 Processing helix chain 'N' and resid 47 through 70 Processing helix chain 'N' and resid 84 through 117 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 119 through 127 Processing helix chain 'N' and resid 150 through 159 removed outlier: 4.241A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 197 Processing helix chain 'N' and resid 213 through 268 Proline residue: N 228 - end of helix removed outlier: 6.086A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 296 Proline residue: N 288 - end of helix removed outlier: 3.655A pdb=" N ALA N 295 " --> pdb=" O GLU N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 329 through 336 removed outlier: 3.637A pdb=" N LEU N 332 " --> pdb=" O PRO N 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU N 333 " --> pdb=" O PHE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 362 Proline residue: N 352 - end of helix Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 366 through 384 Processing helix chain 'N' and resid 400 through 424 removed outlier: 3.875A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 488 Processing helix chain 'N' and resid 492 through 515 Processing helix chain 'N' and resid 522 through 542 removed outlier: 4.760A pdb=" N GLY N 526 " --> pdb=" O GLY N 522 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU N 527 " --> pdb=" O TRP N 523 " (cutoff:3.500A) Processing helix chain 'N' and resid 548 through 587 removed outlier: 4.438A pdb=" N HIS N 561 " --> pdb=" O HIS N 557 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE N 562 " --> pdb=" O ILE N 558 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE N 564 " --> pdb=" O SER N 560 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 594 through 631 removed outlier: 5.287A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.019A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 47 removed outlier: 4.155A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 79 removed outlier: 3.678A pdb=" N PHE O 52 " --> pdb=" O ARG O 49 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY O 53 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU O 61 " --> pdb=" O PHE O 58 " (cutoff:3.500A) Proline residue: O 62 - end of helix removed outlier: 3.672A pdb=" N LEU O 65 " --> pdb=" O PRO O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 47 removed outlier: 4.157A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 78 removed outlier: 5.221A pdb=" N GLY P 53 " --> pdb=" O SER P 50 " (cutoff:3.500A) Proline residue: P 62 - end of helix removed outlier: 3.586A pdb=" N LEU P 65 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 47 removed outlier: 4.133A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 78 Proline residue: Q 62 - end of helix removed outlier: 5.611A pdb=" N LEU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 47 removed outlier: 4.078A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 79 removed outlier: 4.490A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 5.448A pdb=" N LEU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL R 66 " --> pdb=" O PRO R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 47 removed outlier: 4.153A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 79 removed outlier: 4.695A pdb=" N GLY S 53 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR S 54 " --> pdb=" O ASN S 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 55 " --> pdb=" O PHE S 52 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.665A pdb=" N LEU S 65 " --> pdb=" O PRO S 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 47 removed outlier: 3.701A pdb=" N ILE T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 79 Proline residue: T 62 - end of helix removed outlier: 5.585A pdb=" N LEU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 47 removed outlier: 4.141A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 79 Proline residue: U 62 - end of helix removed outlier: 5.785A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 47 removed outlier: 4.406A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 79 removed outlier: 4.376A pdb=" N GLY V 53 " --> pdb=" O SER V 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR V 54 " --> pdb=" O ASN V 51 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU V 61 " --> pdb=" O PHE V 58 " (cutoff:3.500A) Proline residue: V 62 - end of helix removed outlier: 3.598A pdb=" N LEU V 65 " --> pdb=" O PRO V 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY V 78 " --> pdb=" O ILE V 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 47 removed outlier: 4.176A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 79 removed outlier: 3.868A pdb=" N PHE W 52 " --> pdb=" O ARG W 49 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY W 53 " --> pdb=" O SER W 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR W 54 " --> pdb=" O ASN W 51 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU W 61 " --> pdb=" O PHE W 58 " (cutoff:3.500A) Proline residue: W 62 - end of helix removed outlier: 3.624A pdb=" N LEU W 65 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 47 removed outlier: 3.777A pdb=" N ILE X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 79 removed outlier: 3.735A pdb=" N PHE X 52 " --> pdb=" O ARG X 49 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY X 53 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR X 54 " --> pdb=" O ASN X 51 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA X 55 " --> pdb=" O PHE X 52 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU X 61 " --> pdb=" O PHE X 58 " (cutoff:3.500A) Proline residue: X 62 - end of helix removed outlier: 3.551A pdb=" N LEU X 65 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 47 removed outlier: 4.263A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 78 Proline residue: Y 62 - end of helix removed outlier: 5.712A pdb=" N LEU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL Y 66 " --> pdb=" O PRO Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 47 removed outlier: 3.908A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 79 Proline residue: Z 62 - end of helix removed outlier: 5.934A pdb=" N LEU Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL Z 66 " --> pdb=" O PRO Z 62 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 5.644A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.909A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 119 through 121 Processing sheet with id= E, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.880A pdb=" N ALA A 405 " --> pdb=" O ALA A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.874A pdb=" N LYS A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.535A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= I, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.829A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN B 290 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY B 254 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL B 251 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 321 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 253 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N MET B 323 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS B 255 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP B 325 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.786A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 134 through 139 removed outlier: 7.076A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.963A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 64 through 66 removed outlier: 5.363A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= P, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.904A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL C 251 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA C 321 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 253 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET C 323 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS C 255 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP C 325 " --> pdb=" O CYS C 255 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 166 removed outlier: 5.427A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.685A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.606A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= U, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.076A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 219 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 221 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= W, first strand: chain 'E' and resid 18 through 22 removed outlier: 3.725A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= Y, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 307 through 312 Processing sheet with id= AA, first strand: chain 'F' and resid 11 through 15 removed outlier: 4.522A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AC, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AD, first strand: chain 'G' and resid 91 through 95 Processing sheet with id= AE, first strand: chain 'H' and resid 45 through 48 Processing sheet with id= AF, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.778A pdb=" N ASN J 165 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 141 through 144 removed outlier: 6.708A pdb=" N VAL L 155 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU L 121 " --> pdb=" O ARG L 153 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG L 153 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA L 123 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY L 151 " --> pdb=" O ALA L 123 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL L 152 " --> pdb=" O ASN L 165 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR L 161 " --> pdb=" O GLY L 156 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 276 through 282 Processing sheet with id= AI, first strand: chain 'N' and resid 141 through 145 Processing sheet with id= AJ, first strand: chain 'N' and resid 389 through 391 2380 hydrogen bonds defined for protein. 6501 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: 16.50 Time building geometry restraints manager: 20.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8120 1.32 - 1.44: 8905 1.44 - 1.56: 23496 1.56 - 1.69: 7 1.69 - 1.81: 194 Bond restraints: 40722 Sorted by residual: bond pdb=" CA GLU F 7 " pdb=" C GLU F 7 " ideal model delta sigma weight residual 1.524 1.478 0.047 1.22e-02 6.72e+03 1.46e+01 bond pdb=" CB TYR I 73 " pdb=" CG TYR I 73 " ideal model delta sigma weight residual 1.512 1.434 0.078 2.20e-02 2.07e+03 1.26e+01 bond pdb=" CB TYR F 8 " pdb=" CG TYR F 8 " ideal model delta sigma weight residual 1.512 1.438 0.074 2.20e-02 2.07e+03 1.13e+01 bond pdb=" CG LEU B 322 " pdb=" CD1 LEU B 322 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.12e+01 bond pdb=" CB GLN J 162 " pdb=" CG GLN J 162 " ideal model delta sigma weight residual 1.520 1.420 0.100 3.00e-02 1.11e+03 1.11e+01 ... (remaining 40717 not shown) Histogram of bond angle deviations from ideal: 96.11 - 104.62: 782 104.62 - 113.13: 22150 113.13 - 121.64: 23623 121.64 - 130.15: 8666 130.15 - 138.65: 142 Bond angle restraints: 55363 Sorted by residual: angle pdb=" N GLY N 275 " pdb=" CA GLY N 275 " pdb=" C GLY N 275 " ideal model delta sigma weight residual 111.37 102.30 9.07 1.29e+00 6.01e-01 4.94e+01 angle pdb=" N GLY C 366 " pdb=" CA GLY C 366 " pdb=" C GLY C 366 " ideal model delta sigma weight residual 113.18 129.46 -16.28 2.37e+00 1.78e-01 4.72e+01 angle pdb=" N GLY F 179 " pdb=" CA GLY F 179 " pdb=" C GLY F 179 " ideal model delta sigma weight residual 111.36 104.75 6.61 1.17e+00 7.31e-01 3.19e+01 angle pdb=" N ILE K 23 " pdb=" CA ILE K 23 " pdb=" C ILE K 23 " ideal model delta sigma weight residual 111.81 107.14 4.67 8.60e-01 1.35e+00 2.95e+01 angle pdb=" C ASN C 442 " pdb=" N VAL C 443 " pdb=" CA VAL C 443 " ideal model delta sigma weight residual 122.97 117.71 5.26 9.80e-01 1.04e+00 2.88e+01 ... (remaining 55358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.48: 24271 32.48 - 64.95: 207 64.95 - 97.43: 8 97.43 - 129.91: 0 129.91 - 162.38: 1 Dihedral angle restraints: 24487 sinusoidal: 7995 harmonic: 16492 Sorted by residual: dihedral pdb=" CA ALA H 43 " pdb=" C ALA H 43 " pdb=" N LEU H 44 " pdb=" CA LEU H 44 " ideal model delta harmonic sigma weight residual 180.00 138.92 41.08 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA VAL N 301 " pdb=" C VAL N 301 " pdb=" N VAL N 302 " pdb=" CA VAL N 302 " ideal model delta harmonic sigma weight residual 180.00 -142.00 -38.00 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA PHE G 108 " pdb=" C PHE G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta harmonic sigma weight residual 180.00 143.49 36.51 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 24484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5254 0.087 - 0.174: 1049 0.174 - 0.262: 99 0.262 - 0.349: 15 0.349 - 0.436: 3 Chirality restraints: 6420 Sorted by residual: chirality pdb=" CB ILE F 229 " pdb=" CA ILE F 229 " pdb=" CG1 ILE F 229 " pdb=" CG2 ILE F 229 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASP E 259 " pdb=" N ASP E 259 " pdb=" C ASP E 259 " pdb=" CB ASP E 259 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 6417 not shown) Planarity restraints: 7461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO B 227 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 40 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA L 40 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA L 40 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU L 41 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 393 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO B 394 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " 0.044 5.00e-02 4.00e+02 ... (remaining 7458 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1392 2.68 - 3.23: 39011 3.23 - 3.79: 65261 3.79 - 4.34: 77618 4.34 - 4.90: 132791 Nonbonded interactions: 316073 Sorted by model distance: nonbonded pdb=" O GLU L 36 " pdb=" O LYS L 39 " model vdw 2.125 2.432 nonbonded pdb=" OE1 GLU C 38 " pdb=" OH TYR C 52 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR A 263 " pdb=" O ARG F 124 " model vdw 2.264 2.440 nonbonded pdb=" OE1 GLU B 38 " pdb=" OH TYR B 52 " model vdw 2.268 2.440 nonbonded pdb=" O ASP D 67 " pdb=" OG1 THR D 71 " model vdw 2.277 2.440 ... (remaining 316068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 577) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 5 through 464) selection = (chain 'F' and resid 5 through 464) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 0.140 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: 0.050 Extract box with map and model: 3.780 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 116.450 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.015 0.141 40722 Z= 0.986 Angle : 1.256 16.277 55363 Z= 0.671 Chirality : 0.068 0.436 6420 Planarity : 0.008 0.099 7461 Dihedral : 10.437 162.385 13947 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 0.65 % Allowed : 5.58 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -3.98 (0.09), residues: 5794 helix: -2.25 (0.06), residues: 3174 sheet: -2.21 (0.20), residues: 596 loop : -3.15 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP C 407 HIS 0.022 0.004 HIS F 458 PHE 0.043 0.005 PHE C 205 TYR 0.044 0.004 TYR D 251 ARG 0.024 0.002 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 889 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.9229 (tp40) cc_final: 0.9027 (tt0) REVERT: A 92 GLU cc_start: 0.8884 (tp30) cc_final: 0.8556 (mt-10) REVERT: A 504 ASP cc_start: 0.8582 (t70) cc_final: 0.8354 (t70) REVERT: A 547 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7357 (mtp180) REVERT: A 568 LYS cc_start: 0.9203 (mptm) cc_final: 0.8555 (pttp) REVERT: B 25 TYR cc_start: 0.8986 (m-80) cc_final: 0.8727 (m-80) REVERT: B 81 ASN cc_start: 0.8840 (t0) cc_final: 0.8539 (t0) REVERT: B 127 ASP cc_start: 0.8766 (m-30) cc_final: 0.8332 (m-30) REVERT: B 133 MET cc_start: 0.9194 (ttm) cc_final: 0.8911 (tpp) REVERT: B 156 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8478 (ttt-90) REVERT: B 176 GLU cc_start: 0.8680 (tt0) cc_final: 0.8479 (tp30) REVERT: B 213 ASP cc_start: 0.9418 (p0) cc_final: 0.9148 (p0) REVERT: B 261 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8949 (mt-10) REVERT: B 325 ASP cc_start: 0.8601 (t70) cc_final: 0.8291 (t70) REVERT: B 375 GLU cc_start: 0.9214 (pp20) cc_final: 0.8998 (pp20) REVERT: B 493 ASP cc_start: 0.8929 (t0) cc_final: 0.8308 (m-30) REVERT: B 524 LYS cc_start: 0.9237 (tmmt) cc_final: 0.8929 (tppt) REVERT: B 557 GLU cc_start: 0.9257 (tt0) cc_final: 0.8849 (tp30) REVERT: B 558 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8716 (tp30) REVERT: C 1 MET cc_start: 0.7922 (tmm) cc_final: 0.7621 (tmm) REVERT: C 27 ILE cc_start: 0.9513 (mm) cc_final: 0.9287 (mm) REVERT: C 41 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8776 (tmm-80) REVERT: C 441 GLU cc_start: 0.9475 (tp30) cc_final: 0.8991 (mm-30) REVERT: C 442 ASN cc_start: 0.9263 (m110) cc_final: 0.8651 (t0) REVERT: C 524 LYS cc_start: 0.9286 (ttpp) cc_final: 0.8918 (tmtt) REVERT: D 6 LYS cc_start: 0.8955 (tptm) cc_final: 0.8737 (tppt) REVERT: D 8 TYR cc_start: 0.8893 (m-80) cc_final: 0.8059 (m-80) REVERT: D 49 GLU cc_start: 0.9068 (tt0) cc_final: 0.8715 (tm-30) REVERT: D 222 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8094 (t0) REVERT: D 223 LYS cc_start: 0.8669 (pttm) cc_final: 0.8132 (tptp) REVERT: D 226 ASP cc_start: 0.8711 (p0) cc_final: 0.8400 (p0) REVERT: D 376 LYS cc_start: 0.8753 (ttpm) cc_final: 0.8344 (tptm) REVERT: E 62 GLU cc_start: 0.8961 (pt0) cc_final: 0.8607 (pm20) REVERT: E 275 GLU cc_start: 0.9234 (mp0) cc_final: 0.8892 (mt-10) REVERT: E 318 ASP cc_start: 0.8734 (t0) cc_final: 0.8461 (t0) REVERT: E 376 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8584 (ttpt) REVERT: E 411 TYR cc_start: 0.8495 (m-10) cc_final: 0.8051 (m-10) REVERT: E 450 GLU cc_start: 0.8691 (tp30) cc_final: 0.8366 (tm-30) REVERT: F 79 VAL cc_start: 0.9194 (p) cc_final: 0.8925 (m) REVERT: F 141 MET cc_start: 0.9094 (mtp) cc_final: 0.8837 (mtm) REVERT: F 176 ASP cc_start: 0.9284 (m-30) cc_final: 0.9082 (m-30) REVERT: F 315 SER cc_start: 0.8985 (m) cc_final: 0.8635 (p) REVERT: F 380 ASP cc_start: 0.9238 (m-30) cc_final: 0.9019 (t0) REVERT: G 61 TYR cc_start: 0.8831 (m-80) cc_final: 0.8533 (m-80) REVERT: G 68 GLN cc_start: 0.8150 (mt0) cc_final: 0.7754 (tm-30) REVERT: G 152 GLU cc_start: 0.8818 (pt0) cc_final: 0.8594 (tm-30) REVERT: G 208 GLU cc_start: 0.7529 (tp30) cc_final: 0.6801 (tt0) REVERT: H 52 LEU cc_start: 0.7102 (mp) cc_final: 0.6885 (mt) REVERT: H 61 ARG cc_start: 0.7951 (tmt-80) cc_final: 0.7334 (ttp80) REVERT: H 77 LEU cc_start: 0.6710 (pt) cc_final: 0.6438 (pt) REVERT: I 88 TYR cc_start: 0.7779 (m-10) cc_final: 0.7548 (m-80) REVERT: J 58 ARG cc_start: 0.8328 (mtm180) cc_final: 0.7226 (ttp-170) REVERT: J 97 LYS cc_start: 0.8948 (mttt) cc_final: 0.8675 (mtmt) REVERT: J 106 LYS cc_start: 0.8308 (mttt) cc_final: 0.8062 (tptt) REVERT: J 112 LEU cc_start: 0.8642 (mp) cc_final: 0.8066 (tt) REVERT: K 45 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7063 (tm-30) REVERT: L 11 GLU cc_start: 0.3136 (mt-10) cc_final: 0.2777 (mm-30) REVERT: L 61 GLU cc_start: 0.8543 (pt0) cc_final: 0.8008 (pt0) outliers start: 21 outliers final: 13 residues processed: 908 average time/residue: 0.6653 time to fit residues: 898.3879 Evaluate side-chains 627 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 613 time to evaluate : 4.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 484 optimal weight: 7.9990 chunk 435 optimal weight: 50.0000 chunk 241 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 449 optimal weight: 50.0000 chunk 174 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 521 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 145 HIS A 185 HIS A 239 GLN A 571 GLN B 316 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN C 397 GLN C 496 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 262 ASN D 425 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 363 ASN E 429 ASN F 428 GLN G 3 GLN G 10 ASN ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40722 Z= 0.278 Angle : 0.688 14.807 55363 Z= 0.356 Chirality : 0.044 0.201 6420 Planarity : 0.006 0.078 7461 Dihedral : 6.314 149.245 6292 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.10 % Rotamer: Outliers : 2.81 % Allowed : 11.75 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -1.70 (0.10), residues: 5794 helix: -0.02 (0.09), residues: 3176 sheet: -2.02 (0.20), residues: 603 loop : -2.57 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 187 HIS 0.009 0.001 HIS E 249 PHE 0.016 0.001 PHE C 269 TYR 0.017 0.002 TYR C 184 ARG 0.009 0.001 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 735 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8764 (tt0) REVERT: A 213 ASP cc_start: 0.9108 (p0) cc_final: 0.8600 (m-30) REVERT: A 274 ASP cc_start: 0.8862 (t0) cc_final: 0.8246 (p0) REVERT: A 344 MET cc_start: 0.9363 (tpp) cc_final: 0.9081 (tpp) REVERT: A 465 GLN cc_start: 0.9086 (pp30) cc_final: 0.8767 (tp-100) REVERT: A 466 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 568 LYS cc_start: 0.9134 (mptm) cc_final: 0.8553 (pttp) REVERT: B 25 TYR cc_start: 0.8895 (m-80) cc_final: 0.8647 (m-80) REVERT: B 40 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8933 (mt) REVERT: B 81 ASN cc_start: 0.8914 (t0) cc_final: 0.8604 (t0) REVERT: B 153 VAL cc_start: 0.9187 (t) cc_final: 0.8980 (t) REVERT: B 176 GLU cc_start: 0.8799 (tt0) cc_final: 0.8583 (tp30) REVERT: B 213 ASP cc_start: 0.9231 (p0) cc_final: 0.8984 (p0) REVERT: B 268 GLU cc_start: 0.9051 (pt0) cc_final: 0.8741 (pt0) REVERT: B 375 GLU cc_start: 0.9200 (pp20) cc_final: 0.8994 (pt0) REVERT: B 476 LEU cc_start: 0.9078 (mm) cc_final: 0.8725 (mp) REVERT: B 493 ASP cc_start: 0.8784 (t0) cc_final: 0.8449 (m-30) REVERT: B 524 LYS cc_start: 0.9170 (tmmt) cc_final: 0.8861 (tppt) REVERT: B 557 GLU cc_start: 0.9152 (tt0) cc_final: 0.8765 (tp30) REVERT: B 558 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8566 (tp30) REVERT: C 41 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8377 (ttt180) REVERT: C 264 ASP cc_start: 0.9432 (t70) cc_final: 0.9076 (t70) REVERT: C 341 LEU cc_start: 0.9048 (mt) cc_final: 0.8747 (mt) REVERT: C 441 GLU cc_start: 0.9392 (tp30) cc_final: 0.8939 (mm-30) REVERT: C 509 MET cc_start: 0.8383 (mtm) cc_final: 0.8171 (mtm) REVERT: D 194 MET cc_start: 0.8967 (ptp) cc_final: 0.8744 (ptt) REVERT: D 376 LYS cc_start: 0.8673 (ttpm) cc_final: 0.8365 (tptm) REVERT: E 26 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8026 (t0) REVERT: E 62 GLU cc_start: 0.8947 (pt0) cc_final: 0.8743 (pm20) REVERT: E 275 GLU cc_start: 0.9228 (mp0) cc_final: 0.8960 (mm-30) REVERT: E 318 ASP cc_start: 0.8705 (t0) cc_final: 0.8428 (t0) REVERT: E 411 TYR cc_start: 0.8589 (m-10) cc_final: 0.8120 (m-10) REVERT: E 450 GLU cc_start: 0.8558 (tp30) cc_final: 0.8218 (tm-30) REVERT: F 79 VAL cc_start: 0.9008 (p) cc_final: 0.8700 (m) REVERT: F 142 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8205 (p0) REVERT: F 176 ASP cc_start: 0.9223 (m-30) cc_final: 0.8950 (m-30) REVERT: F 315 SER cc_start: 0.9038 (m) cc_final: 0.8655 (p) REVERT: G 15 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.8715 (ttp-110) REVERT: G 19 ARG cc_start: 0.9163 (mtm110) cc_final: 0.8793 (mtm110) REVERT: G 50 ARG cc_start: 0.8927 (mtp-110) cc_final: 0.8461 (mtp85) REVERT: G 61 TYR cc_start: 0.8713 (m-80) cc_final: 0.8473 (m-80) REVERT: G 68 GLN cc_start: 0.8108 (mt0) cc_final: 0.7703 (tm-30) REVERT: G 165 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8128 (tm-30) REVERT: H 19 GLU cc_start: 0.8148 (tp30) cc_final: 0.7690 (tm-30) REVERT: H 21 TYR cc_start: 0.8597 (m-10) cc_final: 0.8080 (m-10) REVERT: H 54 ASP cc_start: 0.8112 (p0) cc_final: 0.7591 (p0) REVERT: H 61 ARG cc_start: 0.7890 (tmt-80) cc_final: 0.7238 (ttp-110) REVERT: H 85 ASP cc_start: 0.8238 (t0) cc_final: 0.7741 (p0) REVERT: I 76 ARG cc_start: 0.6900 (ttp80) cc_final: 0.6505 (ttp80) REVERT: J 58 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7056 (tmm-80) REVERT: J 97 LYS cc_start: 0.8941 (mttt) cc_final: 0.8593 (mtmt) REVERT: J 102 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: J 107 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7133 (pp) REVERT: J 112 LEU cc_start: 0.8515 (mp) cc_final: 0.8039 (tt) REVERT: J 153 ARG cc_start: 0.6872 (ptm-80) cc_final: 0.6501 (ptm160) REVERT: J 181 LYS cc_start: 0.7222 (ptpp) cc_final: 0.6988 (ptpp) REVERT: L 11 GLU cc_start: 0.3098 (mt-10) cc_final: 0.2812 (mm-30) REVERT: L 61 GLU cc_start: 0.8510 (pt0) cc_final: 0.8266 (pt0) REVERT: L 82 GLU cc_start: 0.9055 (tp30) cc_final: 0.8644 (tp30) REVERT: L 85 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8346 (ttp80) outliers start: 91 outliers final: 52 residues processed: 795 average time/residue: 0.6075 time to fit residues: 743.5334 Evaluate side-chains 684 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 626 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 429 ASN Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 289 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 433 optimal weight: 30.0000 chunk 354 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 522 optimal weight: 40.0000 chunk 564 optimal weight: 50.0000 chunk 465 optimal weight: 50.0000 chunk 517 optimal weight: 50.0000 chunk 178 optimal weight: 8.9990 chunk 418 optimal weight: 30.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 442 ASN C 477 GLN C 496 GLN C 571 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN G 3 GLN G 10 ASN H 11 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 40722 Z= 0.537 Angle : 0.775 18.190 55363 Z= 0.397 Chirality : 0.048 0.219 6420 Planarity : 0.006 0.069 7461 Dihedral : 6.178 137.966 6289 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.32 % Favored : 92.66 % Rotamer: Outliers : 4.90 % Allowed : 14.86 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -1.03 (0.11), residues: 5794 helix: 0.65 (0.09), residues: 3173 sheet: -2.00 (0.20), residues: 607 loop : -2.41 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 330 HIS 0.009 0.002 HIS E 249 PHE 0.026 0.002 PHE C 205 TYR 0.022 0.002 TYR F 295 ARG 0.011 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 612 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASP cc_start: 0.9197 (p0) cc_final: 0.8736 (m-30) REVERT: A 274 ASP cc_start: 0.8919 (t0) cc_final: 0.8452 (p0) REVERT: A 344 MET cc_start: 0.9436 (tpp) cc_final: 0.9052 (tpp) REVERT: A 465 GLN cc_start: 0.9126 (pp30) cc_final: 0.8807 (tp-100) REVERT: A 542 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 568 LYS cc_start: 0.9141 (mptm) cc_final: 0.8526 (pttp) REVERT: B 153 VAL cc_start: 0.9204 (t) cc_final: 0.8999 (t) REVERT: B 375 GLU cc_start: 0.9267 (pp20) cc_final: 0.8984 (pt0) REVERT: B 493 ASP cc_start: 0.8850 (t0) cc_final: 0.8462 (m-30) REVERT: B 524 LYS cc_start: 0.9202 (tmmt) cc_final: 0.8887 (tptp) REVERT: B 557 GLU cc_start: 0.9257 (tt0) cc_final: 0.8811 (tp30) REVERT: B 558 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8603 (tp30) REVERT: C 41 ARG cc_start: 0.9025 (tmm-80) cc_final: 0.8369 (ttt180) REVERT: C 112 ASP cc_start: 0.8721 (t0) cc_final: 0.8506 (t70) REVERT: C 441 GLU cc_start: 0.9297 (tp30) cc_final: 0.8975 (mm-30) REVERT: C 478 ASP cc_start: 0.8566 (m-30) cc_final: 0.8215 (p0) REVERT: C 520 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9277 (mm) REVERT: E 26 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8144 (t0) REVERT: E 62 GLU cc_start: 0.9001 (pt0) cc_final: 0.8666 (pm20) REVERT: E 275 GLU cc_start: 0.9272 (mp0) cc_final: 0.8966 (mm-30) REVERT: E 411 TYR cc_start: 0.8808 (m-10) cc_final: 0.8415 (m-10) REVERT: E 450 GLU cc_start: 0.8656 (tp30) cc_final: 0.8302 (tm-30) REVERT: F 79 VAL cc_start: 0.9053 (p) cc_final: 0.8752 (m) REVERT: F 315 SER cc_start: 0.8975 (m) cc_final: 0.8625 (p) REVERT: F 329 THR cc_start: 0.9461 (m) cc_final: 0.9255 (m) REVERT: G 30 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8537 (mttm) REVERT: G 50 ARG cc_start: 0.9065 (mtp-110) cc_final: 0.8630 (mtt-85) REVERT: G 68 GLN cc_start: 0.8113 (mt0) cc_final: 0.7449 (tm-30) REVERT: G 165 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8160 (tm-30) REVERT: H 11 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7871 (pp30) REVERT: H 19 GLU cc_start: 0.8185 (tp30) cc_final: 0.7706 (tm-30) REVERT: H 21 TYR cc_start: 0.8589 (m-10) cc_final: 0.8030 (m-10) REVERT: H 54 ASP cc_start: 0.8155 (p0) cc_final: 0.7598 (p0) REVERT: H 61 ARG cc_start: 0.7811 (tmt-80) cc_final: 0.7202 (ttp-110) REVERT: H 85 ASP cc_start: 0.8442 (t0) cc_final: 0.7708 (p0) REVERT: H 87 GLU cc_start: 0.8724 (mp0) cc_final: 0.8459 (mm-30) REVERT: J 58 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7025 (tmm-80) REVERT: J 107 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7313 (pp) REVERT: J 112 LEU cc_start: 0.8571 (mp) cc_final: 0.8201 (tp) REVERT: J 149 ARG cc_start: 0.6896 (mmm-85) cc_final: 0.5955 (tpt-90) REVERT: K 45 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: L 82 GLU cc_start: 0.9055 (tp30) cc_final: 0.8675 (tp30) outliers start: 159 outliers final: 101 residues processed: 732 average time/residue: 0.5927 time to fit residues: 677.2615 Evaluate side-chains 665 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 557 time to evaluate : 4.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 515 optimal weight: 50.0000 chunk 392 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 chunk 524 optimal weight: 5.9990 chunk 554 optimal weight: 50.0000 chunk 273 optimal weight: 8.9990 chunk 496 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 145 HIS B 397 GLN C 442 ASN C 496 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN G 68 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 40722 Z= 0.244 Angle : 0.626 15.359 55363 Z= 0.318 Chirality : 0.043 0.187 6420 Planarity : 0.005 0.062 7461 Dihedral : 5.690 117.237 6289 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.44 % Favored : 94.55 % Rotamer: Outliers : 3.92 % Allowed : 16.99 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 5794 helix: 1.17 (0.09), residues: 3186 sheet: -1.66 (0.21), residues: 580 loop : -2.24 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 330 HIS 0.004 0.001 HIS F 323 PHE 0.015 0.001 PHE B 574 TYR 0.032 0.001 TYR C 353 ARG 0.014 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 638 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8434 (mtp180) REVERT: A 213 ASP cc_start: 0.9131 (p0) cc_final: 0.8672 (m-30) REVERT: A 274 ASP cc_start: 0.8902 (t0) cc_final: 0.8517 (p0) REVERT: A 424 TRP cc_start: 0.8991 (p90) cc_final: 0.8761 (p90) REVERT: A 465 GLN cc_start: 0.9119 (pp30) cc_final: 0.8837 (tp-100) REVERT: A 540 LEU cc_start: 0.8415 (mp) cc_final: 0.8152 (mt) REVERT: A 568 LYS cc_start: 0.9128 (mptm) cc_final: 0.8540 (pttp) REVERT: B 25 TYR cc_start: 0.8807 (m-80) cc_final: 0.8450 (m-80) REVERT: B 81 ASN cc_start: 0.8974 (t0) cc_final: 0.8646 (t0) REVERT: B 133 MET cc_start: 0.9108 (tpp) cc_final: 0.8782 (tpp) REVERT: B 153 VAL cc_start: 0.9172 (t) cc_final: 0.8970 (t) REVERT: B 375 GLU cc_start: 0.9240 (pp20) cc_final: 0.8980 (pt0) REVERT: B 493 ASP cc_start: 0.8746 (t0) cc_final: 0.8516 (m-30) REVERT: B 524 LYS cc_start: 0.9192 (tmmt) cc_final: 0.8743 (tppt) REVERT: B 557 GLU cc_start: 0.9173 (tt0) cc_final: 0.8770 (tp30) REVERT: B 558 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8473 (tp30) REVERT: C 41 ARG cc_start: 0.8940 (tmm-80) cc_final: 0.8655 (tmm-80) REVERT: C 264 ASP cc_start: 0.9268 (t70) cc_final: 0.8829 (t70) REVERT: C 441 GLU cc_start: 0.9232 (tp30) cc_final: 0.8931 (mm-30) REVERT: C 478 ASP cc_start: 0.8441 (m-30) cc_final: 0.8135 (p0) REVERT: C 492 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8943 (tt0) REVERT: C 520 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9250 (mm) REVERT: D 149 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8451 (pmmt) REVERT: D 319 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: D 345 ARG cc_start: 0.8927 (ptp-110) cc_final: 0.8583 (ptp90) REVERT: E 26 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8135 (t0) REVERT: E 62 GLU cc_start: 0.9083 (pt0) cc_final: 0.8740 (pm20) REVERT: E 275 GLU cc_start: 0.9228 (mp0) cc_final: 0.8942 (mm-30) REVERT: E 450 GLU cc_start: 0.8623 (tp30) cc_final: 0.8168 (tm-30) REVERT: F 79 VAL cc_start: 0.9074 (p) cc_final: 0.8648 (m) REVERT: F 315 SER cc_start: 0.8907 (m) cc_final: 0.8514 (p) REVERT: G 19 ARG cc_start: 0.9160 (mtm110) cc_final: 0.8670 (mtm110) REVERT: G 30 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8477 (mttm) REVERT: G 50 ARG cc_start: 0.9033 (mtp-110) cc_final: 0.8593 (mtt-85) REVERT: G 125 GLU cc_start: 0.9035 (tp30) cc_final: 0.8732 (tp30) REVERT: G 165 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8238 (tm-30) REVERT: G 204 ARG cc_start: 0.8323 (tpt170) cc_final: 0.7692 (tpt170) REVERT: H 51 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (mp) REVERT: H 54 ASP cc_start: 0.8066 (p0) cc_final: 0.7181 (p0) REVERT: H 61 ARG cc_start: 0.7840 (tmt-80) cc_final: 0.7156 (ttp-110) REVERT: H 78 LYS cc_start: 0.7062 (mmtt) cc_final: 0.6831 (mmtt) REVERT: H 85 ASP cc_start: 0.8425 (t0) cc_final: 0.7737 (p0) REVERT: H 103 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7917 (mmmt) REVERT: I 73 TYR cc_start: 0.5399 (t80) cc_final: 0.5109 (t80) REVERT: J 58 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7022 (tmm-80) REVERT: J 107 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7149 (pp) REVERT: J 112 LEU cc_start: 0.8545 (mp) cc_final: 0.8178 (tp) REVERT: J 181 LYS cc_start: 0.7064 (ptpp) cc_final: 0.6828 (ptpp) REVERT: L 82 GLU cc_start: 0.9051 (tp30) cc_final: 0.8655 (tp30) REVERT: L 85 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8536 (ttp-110) REVERT: L 181 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8220 (tmmt) outliers start: 127 outliers final: 83 residues processed: 727 average time/residue: 0.6085 time to fit residues: 691.4053 Evaluate side-chains 669 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 578 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 462 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 413 optimal weight: 7.9990 chunk 228 optimal weight: 30.0000 chunk 473 optimal weight: 50.0000 chunk 383 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 498 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 GLN ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 40722 Z= 0.418 Angle : 0.698 18.786 55363 Z= 0.352 Chirality : 0.046 0.195 6420 Planarity : 0.005 0.061 7461 Dihedral : 5.647 96.125 6289 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.80 % Favored : 93.18 % Rotamer: Outliers : 5.33 % Allowed : 17.11 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5794 helix: 1.32 (0.09), residues: 3180 sheet: -1.66 (0.21), residues: 561 loop : -2.19 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 330 HIS 0.007 0.001 HIS E 249 PHE 0.025 0.002 PHE G 130 TYR 0.020 0.002 TYR D 286 ARG 0.012 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 597 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.9334 (p90) cc_final: 0.8960 (p90) REVERT: A 213 ASP cc_start: 0.9152 (p0) cc_final: 0.8730 (m-30) REVERT: A 274 ASP cc_start: 0.8945 (t0) cc_final: 0.8428 (p0) REVERT: A 459 GLN cc_start: 0.9231 (tp40) cc_final: 0.8906 (tm-30) REVERT: A 465 GLN cc_start: 0.9170 (pp30) cc_final: 0.8865 (tp-100) REVERT: A 542 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 568 LYS cc_start: 0.9136 (mptm) cc_final: 0.8511 (pttp) REVERT: B 133 MET cc_start: 0.9179 (tpp) cc_final: 0.8844 (tpp) REVERT: B 153 VAL cc_start: 0.9166 (t) cc_final: 0.8959 (t) REVERT: B 294 MET cc_start: 0.8924 (mmm) cc_final: 0.8562 (mtt) REVERT: B 375 GLU cc_start: 0.9240 (pp20) cc_final: 0.8973 (pt0) REVERT: B 493 ASP cc_start: 0.8793 (t0) cc_final: 0.8473 (m-30) REVERT: B 524 LYS cc_start: 0.9195 (tmmt) cc_final: 0.8717 (tppt) REVERT: B 557 GLU cc_start: 0.9289 (tt0) cc_final: 0.8817 (tp30) REVERT: B 558 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8593 (tp30) REVERT: C 41 ARG cc_start: 0.8980 (tmm-80) cc_final: 0.8708 (tmm-80) REVERT: C 441 GLU cc_start: 0.9259 (tp30) cc_final: 0.8905 (mm-30) REVERT: C 478 ASP cc_start: 0.8462 (m-30) cc_final: 0.8021 (p0) REVERT: C 492 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8965 (tt0) REVERT: C 520 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9261 (mm) REVERT: D 319 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: D 345 ARG cc_start: 0.9012 (ptp-110) cc_final: 0.8675 (ptp90) REVERT: E 26 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8136 (t0) REVERT: E 62 GLU cc_start: 0.9138 (pt0) cc_final: 0.8843 (pm20) REVERT: E 275 GLU cc_start: 0.9246 (mp0) cc_final: 0.8934 (mm-30) REVERT: E 450 GLU cc_start: 0.8642 (tp30) cc_final: 0.8213 (tm-30) REVERT: F 79 VAL cc_start: 0.9014 (p) cc_final: 0.8611 (m) REVERT: F 177 LEU cc_start: 0.8363 (mm) cc_final: 0.8162 (mm) REVERT: F 315 SER cc_start: 0.8934 (m) cc_final: 0.8570 (p) REVERT: G 19 ARG cc_start: 0.9179 (mtm110) cc_final: 0.8695 (mtm110) REVERT: G 61 TYR cc_start: 0.8818 (m-80) cc_final: 0.8554 (m-80) REVERT: G 125 GLU cc_start: 0.9021 (tp30) cc_final: 0.8719 (tp30) REVERT: G 165 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8271 (tm-30) REVERT: H 51 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8344 (mp) REVERT: H 54 ASP cc_start: 0.7673 (p0) cc_final: 0.7109 (p0) REVERT: H 57 ARG cc_start: 0.6614 (mpt90) cc_final: 0.5545 (mmt90) REVERT: H 61 ARG cc_start: 0.7870 (tmt-80) cc_final: 0.7189 (ttp-110) REVERT: H 85 ASP cc_start: 0.8431 (t0) cc_final: 0.7792 (p0) REVERT: I 73 TYR cc_start: 0.5224 (t80) cc_final: 0.4946 (t80) REVERT: J 58 ARG cc_start: 0.8168 (mtm180) cc_final: 0.6969 (tmm-80) REVERT: J 112 LEU cc_start: 0.8567 (mp) cc_final: 0.8213 (tp) REVERT: L 82 GLU cc_start: 0.9065 (tp30) cc_final: 0.8676 (tp30) REVERT: L 85 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8569 (ttp-110) outliers start: 173 outliers final: 124 residues processed: 725 average time/residue: 0.5714 time to fit residues: 653.7361 Evaluate side-chains 683 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 553 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 186 optimal weight: 7.9990 chunk 499 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 555 optimal weight: 6.9990 chunk 461 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 40722 Z= 0.324 Angle : 0.657 18.687 55363 Z= 0.330 Chirality : 0.044 0.171 6420 Planarity : 0.005 0.059 7461 Dihedral : 5.503 83.687 6289 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.70 % Rotamer: Outliers : 5.30 % Allowed : 17.48 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5794 helix: 1.47 (0.09), residues: 3180 sheet: -1.58 (0.21), residues: 553 loop : -2.10 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.004 0.001 HIS J 130 PHE 0.016 0.001 PHE G 130 TYR 0.020 0.001 TYR D 13 ARG 0.013 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 587 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.9334 (p90) cc_final: 0.9032 (p90) REVERT: A 213 ASP cc_start: 0.9085 (p0) cc_final: 0.8659 (m-30) REVERT: A 274 ASP cc_start: 0.8925 (t0) cc_final: 0.8434 (p0) REVERT: A 465 GLN cc_start: 0.9157 (pp30) cc_final: 0.8852 (tp-100) REVERT: A 542 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7949 (mt) REVERT: A 568 LYS cc_start: 0.9123 (mptm) cc_final: 0.8497 (pttp) REVERT: B 25 TYR cc_start: 0.8831 (m-80) cc_final: 0.8464 (m-80) REVERT: B 133 MET cc_start: 0.9155 (tpp) cc_final: 0.8815 (tpp) REVERT: B 147 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8880 (pp) REVERT: B 153 VAL cc_start: 0.9194 (t) cc_final: 0.8976 (t) REVERT: B 375 GLU cc_start: 0.9227 (pp20) cc_final: 0.8965 (tt0) REVERT: B 493 ASP cc_start: 0.8766 (t0) cc_final: 0.8515 (t0) REVERT: B 524 LYS cc_start: 0.9193 (tmmt) cc_final: 0.8718 (tppt) REVERT: B 557 GLU cc_start: 0.9208 (tt0) cc_final: 0.8796 (tp30) REVERT: B 558 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8563 (tp30) REVERT: C 41 ARG cc_start: 0.8929 (tmm-80) cc_final: 0.8655 (tmm-80) REVERT: C 441 GLU cc_start: 0.9245 (tp30) cc_final: 0.8896 (mm-30) REVERT: C 478 ASP cc_start: 0.8405 (m-30) cc_final: 0.8098 (p0) REVERT: C 492 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8950 (tt0) REVERT: C 520 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9260 (mm) REVERT: D 319 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: D 345 ARG cc_start: 0.9005 (ptp-110) cc_final: 0.8660 (ptp90) REVERT: E 26 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8136 (t0) REVERT: E 62 GLU cc_start: 0.9099 (pt0) cc_final: 0.8778 (pm20) REVERT: E 87 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: E 275 GLU cc_start: 0.9229 (mp0) cc_final: 0.8901 (mm-30) REVERT: E 450 GLU cc_start: 0.8651 (tp30) cc_final: 0.8201 (tm-30) REVERT: F 79 VAL cc_start: 0.9049 (p) cc_final: 0.8812 (m) REVERT: F 315 SER cc_start: 0.8865 (m) cc_final: 0.8474 (p) REVERT: G 19 ARG cc_start: 0.9161 (mtm110) cc_final: 0.8659 (mtm110) REVERT: G 61 TYR cc_start: 0.8769 (m-80) cc_final: 0.8524 (m-80) REVERT: G 125 GLU cc_start: 0.9010 (tp30) cc_final: 0.8717 (tp30) REVERT: G 165 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8284 (tm-30) REVERT: H 11 GLN cc_start: 0.7299 (pt0) cc_final: 0.6688 (tm-30) REVERT: H 51 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8317 (mp) REVERT: H 54 ASP cc_start: 0.7754 (p0) cc_final: 0.6993 (p0) REVERT: H 56 GLU cc_start: 0.6421 (pm20) cc_final: 0.5688 (pm20) REVERT: H 57 ARG cc_start: 0.6560 (mpt90) cc_final: 0.5878 (mmt180) REVERT: H 61 ARG cc_start: 0.7911 (tmt-80) cc_final: 0.7217 (ttp-110) REVERT: H 85 ASP cc_start: 0.8504 (t0) cc_final: 0.7915 (p0) REVERT: H 103 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7933 (mmmt) REVERT: I 76 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7328 (ttm110) REVERT: J 58 ARG cc_start: 0.8133 (mtm180) cc_final: 0.6935 (tmm-80) REVERT: J 107 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7268 (pp) REVERT: J 112 LEU cc_start: 0.8551 (mp) cc_final: 0.8203 (tp) REVERT: J 149 ARG cc_start: 0.6924 (mmm-85) cc_final: 0.6366 (tpt-90) REVERT: L 82 GLU cc_start: 0.9040 (tp30) cc_final: 0.8667 (tp30) REVERT: L 85 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8542 (ttp-110) REVERT: L 141 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7424 (mp0) outliers start: 172 outliers final: 128 residues processed: 712 average time/residue: 0.5838 time to fit residues: 652.2665 Evaluate side-chains 694 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 557 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 535 optimal weight: 50.0000 chunk 62 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 314 optimal weight: 20.0000 chunk 467 optimal weight: 40.0000 chunk 310 optimal weight: 0.9990 chunk 553 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 337 optimal weight: 30.0000 chunk 255 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN C 442 ASN C 496 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 40722 Z= 0.331 Angle : 0.653 17.832 55363 Z= 0.329 Chirality : 0.044 0.175 6420 Planarity : 0.005 0.062 7461 Dihedral : 5.361 72.976 6285 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.59 % Favored : 93.39 % Rotamer: Outliers : 5.27 % Allowed : 18.10 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 5794 helix: 1.55 (0.09), residues: 3192 sheet: -1.52 (0.22), residues: 537 loop : -2.03 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.005 0.001 HIS E 249 PHE 0.017 0.001 PHE G 130 TYR 0.014 0.001 TYR C 353 ARG 0.013 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 587 time to evaluate : 4.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8460 (mtp180) REVERT: A 184 TYR cc_start: 0.9367 (p90) cc_final: 0.9055 (p90) REVERT: A 213 ASP cc_start: 0.9092 (p0) cc_final: 0.8674 (m-30) REVERT: A 274 ASP cc_start: 0.8922 (t0) cc_final: 0.8437 (p0) REVERT: A 424 TRP cc_start: 0.9027 (p90) cc_final: 0.8698 (p90) REVERT: A 459 GLN cc_start: 0.9212 (tp40) cc_final: 0.8919 (tm-30) REVERT: A 465 GLN cc_start: 0.9177 (pp30) cc_final: 0.8867 (tp-100) REVERT: A 568 LYS cc_start: 0.9126 (mptm) cc_final: 0.8514 (pttp) REVERT: B 133 MET cc_start: 0.9161 (tpp) cc_final: 0.8826 (tpp) REVERT: B 147 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8914 (pp) REVERT: B 153 VAL cc_start: 0.9199 (t) cc_final: 0.8986 (t) REVERT: B 375 GLU cc_start: 0.9234 (pp20) cc_final: 0.8955 (tt0) REVERT: B 493 ASP cc_start: 0.8767 (t0) cc_final: 0.8526 (t0) REVERT: B 524 LYS cc_start: 0.9200 (tmmt) cc_final: 0.8712 (tppt) REVERT: B 557 GLU cc_start: 0.9226 (tt0) cc_final: 0.8815 (tp30) REVERT: B 558 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8575 (tp30) REVERT: C 41 ARG cc_start: 0.8915 (tmm-80) cc_final: 0.8643 (tmm-80) REVERT: C 478 ASP cc_start: 0.8429 (m-30) cc_final: 0.8118 (p0) REVERT: C 492 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8940 (tt0) REVERT: C 520 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9236 (mm) REVERT: D 319 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: D 345 ARG cc_start: 0.9002 (ptp-110) cc_final: 0.8661 (ptp90) REVERT: E 26 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8151 (t0) REVERT: E 62 GLU cc_start: 0.9109 (pt0) cc_final: 0.8802 (pm20) REVERT: E 87 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: E 275 GLU cc_start: 0.9234 (mp0) cc_final: 0.8891 (mm-30) REVERT: E 318 ASP cc_start: 0.8640 (t0) cc_final: 0.8305 (t0) REVERT: E 450 GLU cc_start: 0.8645 (tp30) cc_final: 0.8319 (mm-30) REVERT: F 79 VAL cc_start: 0.9083 (p) cc_final: 0.8573 (m) REVERT: F 315 SER cc_start: 0.8812 (m) cc_final: 0.8421 (p) REVERT: G 19 ARG cc_start: 0.9147 (mtm110) cc_final: 0.8649 (mtm110) REVERT: G 61 TYR cc_start: 0.8811 (m-80) cc_final: 0.8529 (m-80) REVERT: G 125 GLU cc_start: 0.8989 (tp30) cc_final: 0.8702 (tp30) REVERT: G 165 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8267 (tm-30) REVERT: H 51 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8311 (mp) REVERT: H 54 ASP cc_start: 0.7799 (p0) cc_final: 0.7226 (p0) REVERT: H 56 GLU cc_start: 0.6573 (pm20) cc_final: 0.5988 (pm20) REVERT: H 57 ARG cc_start: 0.6558 (mpt90) cc_final: 0.5892 (mmt90) REVERT: H 61 ARG cc_start: 0.7925 (tmt-80) cc_final: 0.7307 (ttp-110) REVERT: H 85 ASP cc_start: 0.8535 (t0) cc_final: 0.7942 (p0) REVERT: H 103 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7927 (mmmt) REVERT: I 22 LEU cc_start: 0.1654 (OUTLIER) cc_final: 0.1428 (tp) REVERT: J 58 ARG cc_start: 0.8150 (mtm180) cc_final: 0.6931 (tmm-80) REVERT: J 107 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7297 (pp) REVERT: J 112 LEU cc_start: 0.8555 (mp) cc_final: 0.8198 (tp) REVERT: K 22 LEU cc_start: 0.2398 (OUTLIER) cc_final: 0.2170 (mm) REVERT: L 61 GLU cc_start: 0.8603 (pt0) cc_final: 0.8369 (pp20) REVERT: L 82 GLU cc_start: 0.9035 (tp30) cc_final: 0.8672 (tp30) REVERT: L 85 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8565 (ttp-110) REVERT: L 141 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7475 (mp0) outliers start: 171 outliers final: 142 residues processed: 716 average time/residue: 0.5975 time to fit residues: 675.7710 Evaluate side-chains 701 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 549 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 342 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 351 optimal weight: 3.9990 chunk 376 optimal weight: 30.0000 chunk 273 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 434 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN C 442 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40722 Z= 0.233 Angle : 0.618 15.800 55363 Z= 0.310 Chirality : 0.043 0.172 6420 Planarity : 0.004 0.061 7461 Dihedral : 5.181 65.576 6285 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.44 % Favored : 94.55 % Rotamer: Outliers : 4.53 % Allowed : 19.36 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 5794 helix: 1.70 (0.09), residues: 3195 sheet: -1.44 (0.22), residues: 549 loop : -1.88 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 187 HIS 0.004 0.001 HIS J 130 PHE 0.013 0.001 PHE C 406 TYR 0.026 0.001 TYR I 73 ARG 0.015 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 618 time to evaluate : 4.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8464 (mtp180) REVERT: A 184 TYR cc_start: 0.9335 (p90) cc_final: 0.8931 (p90) REVERT: A 213 ASP cc_start: 0.9014 (p0) cc_final: 0.8604 (m-30) REVERT: A 238 GLN cc_start: 0.9077 (mt0) cc_final: 0.8832 (mt0) REVERT: A 274 ASP cc_start: 0.8898 (t0) cc_final: 0.8474 (p0) REVERT: A 424 TRP cc_start: 0.8956 (p90) cc_final: 0.8698 (p90) REVERT: A 459 GLN cc_start: 0.9219 (tp40) cc_final: 0.8856 (tm-30) REVERT: A 465 GLN cc_start: 0.9175 (pp30) cc_final: 0.8886 (tp-100) REVERT: A 568 LYS cc_start: 0.9105 (mptm) cc_final: 0.8508 (pttp) REVERT: A 575 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7489 (ttpp) REVERT: B 25 TYR cc_start: 0.8807 (m-80) cc_final: 0.8427 (m-80) REVERT: B 133 MET cc_start: 0.9136 (tpp) cc_final: 0.8695 (tpp) REVERT: B 147 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8881 (pp) REVERT: B 153 VAL cc_start: 0.9167 (t) cc_final: 0.8959 (t) REVERT: B 375 GLU cc_start: 0.9216 (pp20) cc_final: 0.8962 (tt0) REVERT: B 481 ARG cc_start: 0.9111 (tmm-80) cc_final: 0.8810 (ttm110) REVERT: B 493 ASP cc_start: 0.8702 (t0) cc_final: 0.8485 (t0) REVERT: B 524 LYS cc_start: 0.9185 (tmmt) cc_final: 0.8686 (tppt) REVERT: B 546 GLU cc_start: 0.8933 (pm20) cc_final: 0.8713 (pm20) REVERT: B 557 GLU cc_start: 0.9231 (tt0) cc_final: 0.8801 (tp30) REVERT: B 558 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8549 (tp30) REVERT: C 1 MET cc_start: 0.7466 (tmm) cc_final: 0.7097 (tmm) REVERT: C 41 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8583 (tmm-80) REVERT: C 287 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8765 (mt) REVERT: C 413 LEU cc_start: 0.9185 (mt) cc_final: 0.8943 (mt) REVERT: C 478 ASP cc_start: 0.8396 (m-30) cc_final: 0.8077 (p0) REVERT: C 492 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8969 (tt0) REVERT: C 520 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9248 (mm) REVERT: C 565 GLU cc_start: 0.8818 (tp30) cc_final: 0.8531 (tp30) REVERT: D 36 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8264 (ttpt) REVERT: D 149 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8516 (pmmt) REVERT: D 319 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: D 345 ARG cc_start: 0.8964 (ptp-110) cc_final: 0.8640 (ptp90) REVERT: E 26 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8137 (t0) REVERT: E 41 ARG cc_start: 0.8518 (tmt90) cc_final: 0.8281 (ttt90) REVERT: E 62 GLU cc_start: 0.9080 (pt0) cc_final: 0.8851 (pm20) REVERT: E 275 GLU cc_start: 0.9224 (mp0) cc_final: 0.8888 (mm-30) REVERT: E 318 ASP cc_start: 0.8601 (t0) cc_final: 0.8282 (t0) REVERT: E 413 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8763 (mp10) REVERT: E 450 GLU cc_start: 0.8663 (tp30) cc_final: 0.8327 (mm-30) REVERT: F 79 VAL cc_start: 0.9089 (p) cc_final: 0.8624 (m) REVERT: F 315 SER cc_start: 0.8890 (m) cc_final: 0.8484 (p) REVERT: G 125 GLU cc_start: 0.8984 (tp30) cc_final: 0.8690 (tp30) REVERT: G 165 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8224 (tm-30) REVERT: H 9 THR cc_start: 0.7281 (m) cc_final: 0.6643 (p) REVERT: H 51 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8294 (mp) REVERT: H 54 ASP cc_start: 0.7766 (p0) cc_final: 0.7143 (p0) REVERT: H 56 GLU cc_start: 0.6381 (pm20) cc_final: 0.5825 (pm20) REVERT: H 57 ARG cc_start: 0.6749 (mpt90) cc_final: 0.6115 (mmt90) REVERT: H 61 ARG cc_start: 0.7831 (tmt-80) cc_final: 0.7184 (ttp-110) REVERT: H 63 MET cc_start: 0.7646 (tpp) cc_final: 0.6992 (tpt) REVERT: H 85 ASP cc_start: 0.8488 (t0) cc_final: 0.7880 (p0) REVERT: H 96 LYS cc_start: 0.8557 (tppt) cc_final: 0.8066 (pttt) REVERT: H 103 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7929 (mmmt) REVERT: I 22 LEU cc_start: 0.1685 (OUTLIER) cc_final: 0.1482 (tp) REVERT: J 58 ARG cc_start: 0.8176 (mtm180) cc_final: 0.6974 (tmm-80) REVERT: J 107 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7288 (pp) REVERT: J 112 LEU cc_start: 0.8511 (mp) cc_final: 0.8138 (tp) REVERT: J 119 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7664 (tttp) REVERT: J 149 ARG cc_start: 0.6972 (mmm-85) cc_final: 0.6416 (tpt-90) REVERT: K 22 LEU cc_start: 0.2519 (OUTLIER) cc_final: 0.2309 (mm) REVERT: L 61 GLU cc_start: 0.8559 (pt0) cc_final: 0.8330 (pp20) REVERT: L 82 GLU cc_start: 0.9053 (tp30) cc_final: 0.8717 (tp30) REVERT: L 85 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8570 (ttp-110) REVERT: L 141 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7463 (mp0) outliers start: 147 outliers final: 111 residues processed: 731 average time/residue: 0.5890 time to fit residues: 676.8910 Evaluate side-chains 698 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 574 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 503 optimal weight: 6.9990 chunk 530 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 chunk 515 optimal weight: 5.9990 chunk 529 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 404 optimal weight: 50.0000 chunk 158 optimal weight: 9.9990 chunk 465 optimal weight: 40.0000 chunk 487 optimal weight: 40.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 GLN G 22 GLN G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 40722 Z= 0.424 Angle : 0.701 18.836 55363 Z= 0.355 Chirality : 0.046 0.182 6420 Planarity : 0.005 0.083 7461 Dihedral : 5.319 63.219 6285 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 5.18 % Allowed : 19.12 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 5794 helix: 1.68 (0.09), residues: 3187 sheet: -1.58 (0.21), residues: 546 loop : -1.89 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 187 HIS 0.006 0.001 HIS A 283 PHE 0.018 0.002 PHE G 130 TYR 0.031 0.002 TYR I 73 ARG 0.017 0.001 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 573 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.9379 (p90) cc_final: 0.9092 (p90) REVERT: A 213 ASP cc_start: 0.9064 (p0) cc_final: 0.8682 (m-30) REVERT: A 274 ASP cc_start: 0.8929 (t0) cc_final: 0.8431 (p0) REVERT: A 459 GLN cc_start: 0.9258 (tp40) cc_final: 0.8896 (tm-30) REVERT: A 465 GLN cc_start: 0.9206 (pp30) cc_final: 0.8933 (tp-100) REVERT: A 568 LYS cc_start: 0.9129 (mptm) cc_final: 0.8526 (pttp) REVERT: B 133 MET cc_start: 0.9200 (tpp) cc_final: 0.8840 (tpp) REVERT: B 147 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8904 (pp) REVERT: B 153 VAL cc_start: 0.9219 (t) cc_final: 0.9012 (t) REVERT: B 375 GLU cc_start: 0.9231 (pp20) cc_final: 0.8969 (pt0) REVERT: B 493 ASP cc_start: 0.8752 (t0) cc_final: 0.8496 (m-30) REVERT: B 524 LYS cc_start: 0.9215 (tmmt) cc_final: 0.8701 (tppt) REVERT: B 546 GLU cc_start: 0.8969 (pm20) cc_final: 0.8732 (pm20) REVERT: B 557 GLU cc_start: 0.9261 (tt0) cc_final: 0.8813 (tp30) REVERT: B 558 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8576 (tp30) REVERT: C 41 ARG cc_start: 0.8940 (tmm-80) cc_final: 0.8673 (tmm-80) REVERT: C 413 LEU cc_start: 0.9169 (mt) cc_final: 0.8893 (mt) REVERT: C 478 ASP cc_start: 0.8508 (m-30) cc_final: 0.8191 (p0) REVERT: C 492 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8978 (tt0) REVERT: C 520 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9239 (mm) REVERT: D 36 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8280 (ttpt) REVERT: D 319 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: E 26 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8208 (t0) REVERT: E 62 GLU cc_start: 0.9120 (pt0) cc_final: 0.8803 (pm20) REVERT: E 275 GLU cc_start: 0.9253 (mp0) cc_final: 0.8908 (mm-30) REVERT: E 318 ASP cc_start: 0.8616 (t0) cc_final: 0.8267 (t0) REVERT: E 392 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9183 (tt) REVERT: E 450 GLU cc_start: 0.8700 (tp30) cc_final: 0.8367 (mm-30) REVERT: F 79 VAL cc_start: 0.9023 (p) cc_final: 0.8679 (m) REVERT: F 315 SER cc_start: 0.8799 (m) cc_final: 0.8420 (p) REVERT: G 13 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8622 (tm-30) REVERT: G 19 ARG cc_start: 0.9172 (mtm110) cc_final: 0.8732 (mtm110) REVERT: G 61 TYR cc_start: 0.8923 (m-80) cc_final: 0.8720 (m-80) REVERT: G 125 GLU cc_start: 0.9015 (tp30) cc_final: 0.8721 (tp30) REVERT: G 165 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8257 (tm-30) REVERT: G 177 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8743 (mtm-85) REVERT: H 9 THR cc_start: 0.6726 (m) cc_final: 0.6257 (p) REVERT: H 51 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8291 (mp) REVERT: H 54 ASP cc_start: 0.7899 (p0) cc_final: 0.7437 (p0) REVERT: H 56 GLU cc_start: 0.6638 (pm20) cc_final: 0.6346 (pm20) REVERT: H 61 ARG cc_start: 0.7905 (tmt-80) cc_final: 0.7256 (ttp-110) REVERT: H 85 ASP cc_start: 0.8553 (t0) cc_final: 0.7886 (p0) REVERT: H 96 LYS cc_start: 0.8372 (tppt) cc_final: 0.8006 (pttt) REVERT: H 103 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7925 (mmmt) REVERT: I 22 LEU cc_start: 0.1674 (OUTLIER) cc_final: 0.1460 (tp) REVERT: I 74 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7977 (mmm160) REVERT: J 58 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7058 (tmm-80) REVERT: J 107 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7356 (pp) REVERT: J 112 LEU cc_start: 0.8438 (mp) cc_final: 0.8092 (tp) REVERT: J 149 ARG cc_start: 0.6958 (mmm-85) cc_final: 0.6417 (tpt-90) REVERT: K 22 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.2458 (mm) REVERT: L 82 GLU cc_start: 0.9034 (tp30) cc_final: 0.8683 (tp30) REVERT: L 85 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8588 (ttp-110) REVERT: L 141 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7412 (mp0) outliers start: 168 outliers final: 142 residues processed: 702 average time/residue: 0.5590 time to fit residues: 618.7913 Evaluate side-chains 719 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 566 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 513 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 545 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 258 optimal weight: 7.9990 chunk 378 optimal weight: 30.0000 chunk 571 optimal weight: 50.0000 chunk 526 optimal weight: 50.0000 chunk 455 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 351 optimal weight: 5.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 571 GLN C 442 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 40722 Z= 0.398 Angle : 0.693 18.641 55363 Z= 0.352 Chirality : 0.046 0.182 6420 Planarity : 0.005 0.075 7461 Dihedral : 5.354 59.711 6285 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.63 % Favored : 93.36 % Rotamer: Outliers : 4.96 % Allowed : 19.70 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 5794 helix: 1.68 (0.09), residues: 3187 sheet: -1.58 (0.21), residues: 552 loop : -1.89 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 187 HIS 0.005 0.001 HIS J 130 PHE 0.017 0.002 PHE C 406 TYR 0.032 0.002 TYR I 73 ARG 0.016 0.001 ARG C 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 567 time to evaluate : 4.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.9367 (p90) cc_final: 0.9060 (p90) REVERT: A 213 ASP cc_start: 0.9055 (p0) cc_final: 0.8672 (m-30) REVERT: A 274 ASP cc_start: 0.8929 (t0) cc_final: 0.8426 (p0) REVERT: A 459 GLN cc_start: 0.9247 (tp40) cc_final: 0.8874 (tm-30) REVERT: A 465 GLN cc_start: 0.9240 (pp30) cc_final: 0.8988 (tp-100) REVERT: A 568 LYS cc_start: 0.9134 (mptm) cc_final: 0.8517 (pttp) REVERT: B 133 MET cc_start: 0.9181 (tpp) cc_final: 0.8790 (tpp) REVERT: B 147 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8933 (pp) REVERT: B 153 VAL cc_start: 0.9198 (t) cc_final: 0.8992 (t) REVERT: B 524 LYS cc_start: 0.9208 (tmmt) cc_final: 0.8692 (tppt) REVERT: B 557 GLU cc_start: 0.9260 (tt0) cc_final: 0.8820 (tp30) REVERT: B 558 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8595 (tp30) REVERT: C 1 MET cc_start: 0.7566 (tmm) cc_final: 0.7201 (tmm) REVERT: C 41 ARG cc_start: 0.8950 (tmm-80) cc_final: 0.8690 (tmm-80) REVERT: C 413 LEU cc_start: 0.9162 (mt) cc_final: 0.8899 (mt) REVERT: C 478 ASP cc_start: 0.8491 (m-30) cc_final: 0.8179 (p0) REVERT: C 492 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8975 (tt0) REVERT: C 520 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9231 (mm) REVERT: D 36 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8287 (ttpt) REVERT: D 319 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: D 345 ARG cc_start: 0.9119 (ptp90) cc_final: 0.8670 (ptp90) REVERT: E 26 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8228 (t0) REVERT: E 41 ARG cc_start: 0.8611 (tmt90) cc_final: 0.8359 (ttt90) REVERT: E 62 GLU cc_start: 0.9127 (pt0) cc_final: 0.8894 (pm20) REVERT: E 275 GLU cc_start: 0.9259 (mp0) cc_final: 0.8911 (mm-30) REVERT: E 318 ASP cc_start: 0.8544 (t0) cc_final: 0.8194 (t0) REVERT: E 392 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9183 (tt) REVERT: E 450 GLU cc_start: 0.8698 (tp30) cc_final: 0.8365 (mm-30) REVERT: F 79 VAL cc_start: 0.9016 (p) cc_final: 0.8672 (m) REVERT: F 315 SER cc_start: 0.8844 (m) cc_final: 0.8472 (p) REVERT: G 19 ARG cc_start: 0.9155 (mtm110) cc_final: 0.8674 (mtm-85) REVERT: G 125 GLU cc_start: 0.9014 (tp30) cc_final: 0.8723 (tp30) REVERT: G 165 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8231 (tm-30) REVERT: H 51 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8274 (mp) REVERT: H 54 ASP cc_start: 0.8009 (p0) cc_final: 0.7396 (p0) REVERT: H 56 GLU cc_start: 0.6946 (pm20) cc_final: 0.6346 (pm20) REVERT: H 61 ARG cc_start: 0.7785 (tmt-80) cc_final: 0.7247 (ttp-110) REVERT: H 85 ASP cc_start: 0.8534 (t0) cc_final: 0.7915 (p0) REVERT: I 22 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.1668 (tp) REVERT: I 74 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7906 (mmm160) REVERT: J 58 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7088 (tmm-80) REVERT: J 107 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7398 (pp) REVERT: J 112 LEU cc_start: 0.8536 (mp) cc_final: 0.8180 (tp) REVERT: J 149 ARG cc_start: 0.6968 (mmm-85) cc_final: 0.6429 (tpt-90) REVERT: L 61 GLU cc_start: 0.8610 (pt0) cc_final: 0.8289 (pp20) REVERT: L 82 GLU cc_start: 0.9054 (tp30) cc_final: 0.8708 (tp30) REVERT: L 85 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8621 (ttp-110) REVERT: L 141 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7399 (mp0) outliers start: 161 outliers final: 146 residues processed: 686 average time/residue: 0.5883 time to fit residues: 637.5530 Evaluate side-chains 708 residues out of total 4580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 552 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 408 ASP Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 279 optimal weight: 0.7980 chunk 361 optimal weight: 7.9990 chunk 485 optimal weight: 50.0000 chunk 139 optimal weight: 0.9980 chunk 419 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 456 optimal weight: 50.0000 chunk 190 optimal weight: 8.9990 chunk 468 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098513 restraints weight = 75513.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101251 restraints weight = 39254.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102546 restraints weight = 25626.287| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 40722 Z= 0.248 Angle : 0.634 15.894 55363 Z= 0.320 Chirality : 0.043 0.164 6420 Planarity : 0.004 0.073 7461 Dihedral : 5.149 58.558 6285 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.94 % Favored : 94.05 % Rotamer: Outliers : 4.47 % Allowed : 20.54 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.12), residues: 5794 helix: 1.82 (0.09), residues: 3195 sheet: -1.42 (0.21), residues: 561 loop : -1.80 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 187 HIS 0.004 0.001 HIS F 323 PHE 0.014 0.001 PHE C 406 TYR 0.035 0.001 TYR I 73 ARG 0.017 0.001 ARG C 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10681.08 seconds wall clock time: 197 minutes 55.49 seconds (11875.49 seconds total)