Starting phenix.real_space_refine on Tue Apr 16 09:21:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r10_4703/04_2024/6r10_4703_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r10_4703/04_2024/6r10_4703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r10_4703/04_2024/6r10_4703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r10_4703/04_2024/6r10_4703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r10_4703/04_2024/6r10_4703_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r10_4703/04_2024/6r10_4703_updated.pdb" } resolution = 4.3 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= 0.012 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 101 5.16 5 C 23944 2.51 5 N 7025 2.21 5 O 7447 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 89": "NH1" <-> "NH2" Residue "A ARG 113": "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 364": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 481": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F ARG 410": "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 146": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38522 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: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "F" 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: "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: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 511 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 23, 'ARG:plan': 11, 'ASP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "J" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 922 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 3, 'GLU:plan': 30, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 309 Chain: "K" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 494 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 23, 'ARG:plan': 11, 'ASP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "L" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 926 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 3, 'GLU:plan': 30, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 309 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: "A" 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: "F" 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: 20.26, per 1000 atoms: 0.53 Number of scatterers: 38522 At special positions: 0 Unit cell: (147.56, 147.56, 252.805, 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 101 16.00 P 4 15.00 Mg 1 11.99 O 7447 8.00 N 7025 7.00 C 23944 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: 15.39 Conformation dependent library (CDL) restraints added in 8.1 seconds 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 34 sheets defined 52.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.49 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.737A pdb=" N ARG A 299 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 306 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.682A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.855A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 470 removed outlier: 4.322A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 545 through 552 removed outlier: 4.455A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.646A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.009A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 314 removed outlier: 4.961A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 447 through 470 removed outlier: 4.370A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 494 Processing helix chain 'B' and resid 509 through 532 removed outlier: 4.170A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 540 No H-bonds generated for 'chain 'B' and resid 537 through 540' Processing helix chain 'B' and resid 543 through 551 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 563 through 576 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 243 Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.829A pdb=" N ARG C 299 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 354 through 364 removed outlier: 4.054A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 removed outlier: 5.030A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.405A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 479 through 493 Processing helix chain 'C' and resid 510 through 531 removed outlier: 4.306A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 556 through 572 Proline residue: C 560 - end of helix removed outlier: 3.785A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' 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 160 through 170 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 228 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.761A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.709A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 403 No H-bonds generated for 'chain 'D' and resid 401 through 403' Processing helix chain 'D' and resid 406 through 421 removed outlier: 3.725A pdb=" N ARG D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 4.062A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 161 through 167 Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 228 through 247 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 261 through 271 Processing helix chain 'E' and resid 285 through 295 removed outlier: 4.164A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 295 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.711A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 346 removed outlier: 3.721A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 396 Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 443 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 231 through 247 Proline residue: F 235 - end of helix removed outlier: 3.609A pdb=" N VAL F 241 " --> pdb=" O MET F 237 " (cutoff:3.500A) 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: 3.703A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 291 " --> pdb=" O TYR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.849A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (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 408 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 4.049A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.837A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 124 through 168 removed outlier: 3.811A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 207 Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 56 through 62 Processing helix chain 'H' and resid 86 through 96 Processing helix chain 'I' and resid 19 through 104 removed outlier: 3.830A pdb=" N MET I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 3 through 96 Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 98 through 114 Proline residue: J 101 - end of helix removed outlier: 3.706A pdb=" N ARG J 105 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU J 113 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 4.483A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 167 through 186 removed outlier: 5.562A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 105 Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'L' and resid 3 through 95 Proline residue: L 95 - end of helix Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 126 through 130 Proline residue: L 129 - end of helix No H-bonds generated for 'chain 'L' and resid 126 through 130' Processing helix chain 'L' and resid 132 through 136 Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.115A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN L 184 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 17 removed outlier: 3.915A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 27 Processing helix chain 'M' and resid 34 through 42 Processing helix chain 'M' and resid 44 through 47 Processing helix chain 'M' and resid 54 through 68 Processing helix chain 'M' and resid 70 through 72 No H-bonds generated for 'chain 'M' and resid 70 through 72' Processing helix chain 'M' and resid 79 through 85 Processing helix chain 'M' and resid 89 through 105 Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 146 through 150 Processing helix chain 'M' and resid 163 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 239 through 242 No H-bonds generated for 'chain 'M' and resid 239 through 242' Processing helix chain 'M' and resid 258 through 278 removed outlier: 3.963A pdb=" N GLY M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 308 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 128 Proline residue: N 93 - end of helix removed outlier: 3.543A pdb=" N GLN N 106 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Proline residue: N 121 - end of helix Processing helix chain 'N' and resid 150 through 159 removed outlier: 3.805A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 175 No H-bonds generated for 'chain 'N' and resid 173 through 175' 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: 5.942A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 295 Processing helix chain 'N' and resid 329 through 336 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 385 Processing helix chain 'N' and resid 400 through 424 removed outlier: 4.079A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 488 removed outlier: 3.529A pdb=" N GLY N 471 " --> pdb=" O SER N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 515 Processing helix chain 'N' and resid 522 through 542 removed outlier: 4.444A pdb=" N GLY N 526 " --> pdb=" O GLY N 522 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU N 527 " --> pdb=" O TRP N 523 " (cutoff:3.500A) Processing helix chain 'N' and resid 548 through 586 removed outlier: 4.450A pdb=" N HIS N 561 " --> pdb=" O HIS N 557 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE N 562 " --> pdb=" O ILE N 558 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG N 563 " --> pdb=" O LEU N 559 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE N 564 " --> pdb=" O SER N 560 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 594 through 631 removed outlier: 5.224A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 3.880A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 47 removed outlier: 4.097A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 79 removed outlier: 3.542A pdb=" N PHE O 52 " --> pdb=" O ARG O 49 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY O 53 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR O 54 " --> pdb=" O ASN O 51 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA O 55 " --> pdb=" O PHE O 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU O 61 " --> pdb=" O PHE O 58 " (cutoff:3.500A) Proline residue: O 62 - end of helix removed outlier: 4.232A pdb=" N LEU O 65 " --> pdb=" O PRO O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 47 removed outlier: 4.309A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 78 removed outlier: 4.674A pdb=" N GLY P 53 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR P 54 " --> pdb=" O ASN P 51 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA P 55 " --> pdb=" O PHE P 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU P 61 " --> pdb=" O PHE P 58 " (cutoff:3.500A) Proline residue: P 62 - end of helix removed outlier: 4.801A pdb=" N LEU P 65 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 47 removed outlier: 4.153A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 4.030A 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: 5.702A pdb=" N LEU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 47 removed outlier: 3.982A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 79 removed outlier: 3.655A pdb=" N LEU R 56 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 6.209A pdb=" N LEU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL R 66 " --> pdb=" O PRO R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 47 removed outlier: 4.181A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 79 removed outlier: 3.823A pdb=" N PHE S 52 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY S 53 " --> pdb=" O SER S 50 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR S 54 " --> pdb=" O ASN S 51 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.927A pdb=" N LEU S 65 " --> pdb=" O PRO S 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 47 removed outlier: 3.715A pdb=" N LEU T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.585A 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: 6.205A pdb=" N LEU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 47 removed outlier: 4.127A 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: 5.550A pdb=" N LEU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 47 removed outlier: 4.402A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 79 Proline residue: V 62 - end of helix removed outlier: 5.336A pdb=" N LEU V 65 " --> pdb=" O LEU V 61 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 47 removed outlier: 4.129A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 79 removed outlier: 3.602A pdb=" N PHE W 52 " --> pdb=" O ARG W 49 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY W 53 " --> pdb=" O SER W 50 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR W 54 " --> pdb=" O ASN W 51 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA W 55 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU W 61 " --> pdb=" O PHE W 58 " (cutoff:3.500A) Proline residue: W 62 - end of helix removed outlier: 4.143A pdb=" N LEU W 65 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 47 removed outlier: 4.021A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 79 removed outlier: 3.808A pdb=" N PHE X 52 " --> pdb=" O ARG X 49 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY X 53 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR X 54 " --> pdb=" O ASN X 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA X 55 " --> pdb=" O PHE X 52 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU X 61 " --> pdb=" O PHE X 58 " (cutoff:3.500A) Proline residue: X 62 - end of helix removed outlier: 3.987A pdb=" N LEU X 65 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 45 removed outlier: 4.036A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 79 Proline residue: Y 62 - end of helix removed outlier: 5.832A pdb=" N LEU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL Y 66 " --> pdb=" O PRO Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 47 removed outlier: 3.537A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA Z 16 " --> pdb=" O ARG Z 12 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 61 Processing helix chain 'Z' and resid 64 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 63 through 65 removed outlier: 6.754A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 73 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.000A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS A 255 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 384 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.969A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.748A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 37 through 40 removed outlier: 5.628A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= H, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.859A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.778A pdb=" N ALA B 405 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TRP B 407 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 285 through 289 removed outlier: 6.391A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL B 320 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.841A pdb=" N VAL C 5 " --> pdb=" O LYS C 17 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= M, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.239A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL C 251 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA C 321 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 253 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET C 323 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS C 255 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP C 325 " --> pdb=" O CYS C 255 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 257 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= O, first strand: chain 'C' and resid 134 through 138 removed outlier: 6.816A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.907A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 18 through 22 Processing sheet with id= R, first strand: chain 'D' and resid 81 through 84 Processing sheet with id= S, first strand: chain 'D' and resid 336 through 338 removed outlier: 3.781A pdb=" N MET D 194 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 72 through 75 removed outlier: 3.909A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU E 22 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE E 11 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= V, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= W, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.530A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.600A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= Z, first strand: chain 'F' and resid 152 through 154 Processing sheet with id= AA, first strand: chain 'F' and resid 217 through 222 removed outlier: 6.336A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 90 through 95 Processing sheet with id= AC, first strand: chain 'H' and resid 2 through 4 removed outlier: 4.209A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 142 through 144 removed outlier: 6.415A pdb=" N LEU J 121 " --> pdb=" O GLN J 143 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 141 through 144 Processing sheet with id= AF, first strand: chain 'N' and resid 302 through 306 removed outlier: 4.371A pdb=" N VAL N 302 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA N 11 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 141 through 145 Processing sheet with id= AH, first strand: chain 'N' and resid 389 through 391 2407 hydrogen bonds defined for protein. 6648 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: 14.27 Time building geometry restraints manager: 16.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12041 1.34 - 1.45: 5854 1.45 - 1.57: 20935 1.57 - 1.69: 7 1.69 - 1.81: 190 Bond restraints: 39027 Sorted by residual: bond pdb=" C LEU E 355 " pdb=" N PRO E 356 " ideal model delta sigma weight residual 1.331 1.371 -0.040 7.90e-03 1.60e+04 2.56e+01 bond pdb=" C PHE C 48 " pdb=" N VAL C 49 " ideal model delta sigma weight residual 1.329 1.287 0.042 1.69e-02 3.50e+03 6.08e+00 bond pdb=" C ASP D 353 " pdb=" N PRO D 354 " ideal model delta sigma weight residual 1.336 1.312 0.024 9.80e-03 1.04e+04 5.81e+00 bond pdb=" C GLY F 157 " pdb=" N LEU F 158 " ideal model delta sigma weight residual 1.331 1.263 0.068 2.83e-02 1.25e+03 5.78e+00 bond pdb=" C VAL E 189 " pdb=" N VAL E 190 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.46e-02 4.69e+03 5.18e+00 ... (remaining 39022 not shown) Histogram of bond angle deviations from ideal: 96.39 - 104.70: 714 104.70 - 113.00: 20874 113.00 - 121.30: 21772 121.30 - 129.61: 9734 129.61 - 137.91: 136 Bond angle restraints: 53230 Sorted by residual: angle pdb=" C THR F 371 " pdb=" N ARG F 372 " pdb=" CA ARG F 372 " ideal model delta sigma weight residual 122.19 134.33 -12.14 2.30e+00 1.89e-01 2.79e+01 angle pdb=" C LEU E 361 " pdb=" N MET E 362 " pdb=" CA MET E 362 " ideal model delta sigma weight residual 126.45 135.72 -9.27 1.77e+00 3.19e-01 2.75e+01 angle pdb=" C GLY C 233 " pdb=" N LYS C 234 " pdb=" CA LYS C 234 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ASP F 318 " pdb=" N ASP F 319 " pdb=" CA ASP F 319 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C GLU D 22 " pdb=" N ASN D 23 " pdb=" CA ASN D 23 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 ... (remaining 53225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 23133 35.80 - 71.60: 95 71.60 - 107.40: 6 107.40 - 143.20: 1 143.20 - 179.00: 1 Dihedral angle restraints: 23236 sinusoidal: 6764 harmonic: 16472 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 119.00 -179.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA VAL H 3 " pdb=" C VAL H 3 " pdb=" N ILE H 4 " pdb=" CA ILE H 4 " ideal model delta harmonic sigma weight residual 180.00 145.56 34.44 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA GLY C 142 " pdb=" C GLY C 142 " pdb=" N PHE C 143 " pdb=" CA PHE C 143 " ideal model delta harmonic sigma weight residual -180.00 -146.22 -33.78 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 23233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5607 0.088 - 0.176: 623 0.176 - 0.264: 36 0.264 - 0.353: 3 0.353 - 0.441: 4 Chirality restraints: 6273 Sorted by residual: chirality pdb=" CB ILE E 392 " pdb=" CA ILE E 392 " pdb=" CG1 ILE E 392 " pdb=" CG2 ILE E 392 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB VAL B 378 " pdb=" CA VAL B 378 " pdb=" CG1 VAL B 378 " pdb=" CG2 VAL B 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 6270 not shown) Planarity restraints: 7224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 234 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C LYS C 234 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS C 234 " -0.026 2.00e-02 2.50e+03 pdb=" N THR C 235 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO D 356 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 28 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C CYS B 28 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS B 28 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS B 29 " -0.017 2.00e-02 2.50e+03 ... (remaining 7221 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1373 2.70 - 3.25: 38180 3.25 - 3.80: 63989 3.80 - 4.35: 72969 4.35 - 4.90: 123439 Nonbonded interactions: 299950 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.155 2.170 nonbonded pdb=" O PRO C 386 " pdb=" OH TYR E 331 " model vdw 2.205 2.440 nonbonded pdb=" OE2 GLU A 257 " pdb=" OG SER A 326 " model vdw 2.241 2.440 nonbonded pdb=" OG SER D 431 " pdb=" OE1 GLU D 434 " model vdw 2.247 2.440 nonbonded pdb=" OD1 ASP A 446 " pdb=" OH TYR A 513 " model vdw 2.263 2.440 ... (remaining 299945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 577) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' and resid 2 through 187) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.180 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 101.690 Find NCS groups from input model: 2.480 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:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 39027 Z= 0.428 Angle : 0.964 17.202 53230 Z= 0.531 Chirality : 0.055 0.441 6273 Planarity : 0.007 0.075 7224 Dihedral : 9.708 178.996 12706 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.74 (0.09), residues: 5790 helix: -1.95 (0.07), residues: 3133 sheet: -2.39 (0.20), residues: 530 loop : -3.15 (0.11), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP A 438 HIS 0.014 0.002 HIS F 458 PHE 0.036 0.003 PHE G 130 TYR 0.033 0.003 TYR F 383 ARG 0.010 0.001 ARG D 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1027 time to evaluate : 4.416 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: 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 14 VAL cc_start: 0.8972 (t) cc_final: 0.8732 (m) REVERT: A 35 LEU cc_start: 0.8111 (mp) cc_final: 0.7904 (mp) REVERT: A 92 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8439 (tm-30) REVERT: A 102 ILE cc_start: 0.9129 (mt) cc_final: 0.8852 (mp) REVERT: A 196 GLN cc_start: 0.8803 (tt0) cc_final: 0.8477 (tm-30) REVERT: A 332 GLU cc_start: 0.8862 (tt0) cc_final: 0.8183 (tm-30) REVERT: A 336 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8670 (mm-30) REVERT: A 343 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8672 (mm-30) REVERT: A 459 GLN cc_start: 0.8918 (tp40) cc_final: 0.7964 (tp40) REVERT: A 478 ASP cc_start: 0.8622 (m-30) cc_final: 0.7886 (p0) REVERT: A 480 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8482 (mp0) REVERT: A 492 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8854 (mm-30) REVERT: A 527 GLU cc_start: 0.8853 (pt0) cc_final: 0.8611 (tm-30) REVERT: A 538 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8347 (tp30) REVERT: B 81 ASN cc_start: 0.9306 (t0) cc_final: 0.9088 (t0) REVERT: B 133 MET cc_start: 0.8781 (ttt) cc_final: 0.7947 (mtt) REVERT: B 147 ILE cc_start: 0.9036 (mt) cc_final: 0.8833 (tt) REVERT: B 179 THR cc_start: 0.7849 (m) cc_final: 0.7466 (p) REVERT: B 251 VAL cc_start: 0.9605 (t) cc_final: 0.9371 (p) REVERT: B 287 LEU cc_start: 0.8551 (tt) cc_final: 0.8289 (mp) REVERT: B 291 THR cc_start: 0.9140 (p) cc_final: 0.8840 (p) REVERT: B 328 SER cc_start: 0.9427 (m) cc_final: 0.9020 (p) REVERT: B 342 GLU cc_start: 0.9021 (mp0) cc_final: 0.8789 (mp0) REVERT: B 343 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8571 (mt-10) REVERT: B 391 MET cc_start: 0.7733 (mmt) cc_final: 0.6447 (mmp) REVERT: B 417 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8340 (tpt90) REVERT: B 481 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8457 (tpp80) REVERT: B 541 GLN cc_start: 0.9239 (pt0) cc_final: 0.8783 (pm20) REVERT: B 546 GLU cc_start: 0.9185 (tt0) cc_final: 0.8646 (tm-30) REVERT: B 550 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8412 (ptt-90) REVERT: B 558 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8916 (tm-30) REVERT: C 3 GLN cc_start: 0.8323 (tt0) cc_final: 0.8084 (tm-30) REVERT: C 24 MET cc_start: 0.8270 (mmm) cc_final: 0.7952 (tpp) REVERT: C 74 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8637 (tt0) REVERT: C 101 TYR cc_start: 0.8491 (m-80) cc_final: 0.8163 (m-80) REVERT: C 251 VAL cc_start: 0.9215 (t) cc_final: 0.8890 (m) REVERT: C 268 GLU cc_start: 0.9273 (pt0) cc_final: 0.8415 (tm-30) REVERT: C 282 MET cc_start: 0.8911 (tpt) cc_final: 0.8592 (tpp) REVERT: C 287 LEU cc_start: 0.8784 (pp) cc_final: 0.8440 (tt) REVERT: C 288 ILE cc_start: 0.8897 (mt) cc_final: 0.8672 (mm) REVERT: C 290 ASN cc_start: 0.9190 (t0) cc_final: 0.8656 (t0) REVERT: C 300 GLU cc_start: 0.9486 (tt0) cc_final: 0.8866 (tp30) REVERT: C 304 TYR cc_start: 0.9069 (m-80) cc_final: 0.8794 (m-80) REVERT: C 322 LEU cc_start: 0.9207 (tt) cc_final: 0.8898 (tt) REVERT: C 344 MET cc_start: 0.9128 (mmm) cc_final: 0.8886 (mmm) REVERT: C 410 ASP cc_start: 0.8302 (m-30) cc_final: 0.7782 (m-30) REVERT: C 450 LEU cc_start: 0.8849 (tp) cc_final: 0.8085 (tt) REVERT: C 456 GLU cc_start: 0.8912 (pp20) cc_final: 0.8138 (tp30) REVERT: C 480 GLU cc_start: 0.8738 (pt0) cc_final: 0.8498 (pt0) REVERT: C 498 ASN cc_start: 0.8558 (t0) cc_final: 0.8305 (t0) REVERT: C 538 GLU cc_start: 0.9428 (tt0) cc_final: 0.9202 (tm-30) REVERT: C 558 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7638 (mp0) REVERT: C 567 MET cc_start: 0.8271 (mtt) cc_final: 0.7775 (tpp) REVERT: D 15 SER cc_start: 0.8515 (t) cc_final: 0.8282 (p) REVERT: D 49 GLU cc_start: 0.8993 (tt0) cc_final: 0.8759 (mt-10) REVERT: D 62 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8436 (mm-30) REVERT: D 103 LEU cc_start: 0.8867 (mt) cc_final: 0.8609 (mt) REVERT: D 128 GLU cc_start: 0.7740 (pt0) cc_final: 0.7085 (mt-10) REVERT: D 149 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8377 (ptpt) REVERT: D 154 SER cc_start: 0.9140 (t) cc_final: 0.8788 (p) REVERT: D 182 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7748 (pm20) REVERT: D 206 GLN cc_start: 0.8967 (tt0) cc_final: 0.8726 (tp40) REVERT: D 237 MET cc_start: 0.9168 (mmt) cc_final: 0.8454 (mtp) REVERT: D 290 ASP cc_start: 0.9285 (t0) cc_final: 0.8568 (t0) REVERT: D 316 MET cc_start: 0.9159 (mtm) cc_final: 0.8818 (mtt) REVERT: D 320 ASP cc_start: 0.8683 (p0) cc_final: 0.8473 (p0) REVERT: D 333 THR cc_start: 0.9616 (p) cc_final: 0.9353 (t) REVERT: D 334 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9069 (mm-30) REVERT: D 338 GLN cc_start: 0.9163 (tt0) cc_final: 0.8196 (tp40) REVERT: D 348 ILE cc_start: 0.9145 (mt) cc_final: 0.8933 (mp) REVERT: D 364 ASN cc_start: 0.9349 (m110) cc_final: 0.8933 (t0) REVERT: D 374 ASP cc_start: 0.8496 (p0) cc_final: 0.7733 (p0) REVERT: D 425 GLN cc_start: 0.8599 (tt0) cc_final: 0.8203 (tt0) REVERT: E 58 GLN cc_start: 0.9227 (tt0) cc_final: 0.8837 (tm-30) REVERT: E 77 GLU cc_start: 0.8154 (pt0) cc_final: 0.7928 (pt0) REVERT: E 166 GLN cc_start: 0.9337 (tt0) cc_final: 0.9134 (tt0) REVERT: E 274 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8233 (ptm-80) REVERT: E 280 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7423 (tpp80) REVERT: E 318 ASP cc_start: 0.9032 (t0) cc_final: 0.8741 (t0) REVERT: E 343 LEU cc_start: 0.8978 (mm) cc_final: 0.8720 (mp) REVERT: E 345 ARG cc_start: 0.9189 (mtm-85) cc_final: 0.8787 (mmm160) REVERT: E 364 ASN cc_start: 0.8244 (t0) cc_final: 0.8014 (t0) REVERT: E 372 ARG cc_start: 0.8497 (ttm170) cc_final: 0.8208 (ttm-80) REVERT: E 416 ASP cc_start: 0.8934 (t0) cc_final: 0.8653 (t0) REVERT: E 453 ARG cc_start: 0.8069 (mpt180) cc_final: 0.7856 (mpt180) REVERT: F 34 ASP cc_start: 0.8106 (p0) cc_final: 0.7785 (t0) REVERT: F 46 GLN cc_start: 0.8640 (tt0) cc_final: 0.8414 (tp40) REVERT: F 60 PHE cc_start: 0.9148 (m-10) cc_final: 0.8414 (m-80) REVERT: F 61 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8409 (tm-30) REVERT: F 120 ASN cc_start: 0.9314 (t0) cc_final: 0.8819 (t0) REVERT: F 156 SER cc_start: 0.9114 (m) cc_final: 0.8555 (p) REVERT: F 174 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8194 (mtp85) REVERT: F 207 GLU cc_start: 0.8827 (tp30) cc_final: 0.8489 (tm-30) REVERT: F 227 PRO cc_start: 0.8489 (Cg_exo) cc_final: 0.7903 (Cg_endo) REVERT: F 305 LYS cc_start: 0.9487 (mptm) cc_final: 0.9257 (tttt) REVERT: F 307 SER cc_start: 0.8608 (p) cc_final: 0.8170 (m) REVERT: F 316 MET cc_start: 0.9063 (mtm) cc_final: 0.8782 (mtm) REVERT: F 318 ASP cc_start: 0.9198 (t0) cc_final: 0.8632 (p0) REVERT: F 342 GLU cc_start: 0.9422 (tt0) cc_final: 0.9183 (tp30) REVERT: F 374 ASP cc_start: 0.9082 (p0) cc_final: 0.8346 (t0) REVERT: F 376 LYS cc_start: 0.8586 (mttt) cc_final: 0.8300 (mttt) REVERT: F 410 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7540 (mpt180) REVERT: F 413 GLN cc_start: 0.8744 (mt0) cc_final: 0.8429 (mt0) REVERT: F 446 LEU cc_start: 0.9110 (mt) cc_final: 0.8707 (tp) REVERT: F 454 ILE cc_start: 0.8449 (mt) cc_final: 0.8132 (tt) REVERT: G 5 SER cc_start: 0.8629 (m) cc_final: 0.8410 (p) REVERT: G 13 GLN cc_start: 0.9297 (tt0) cc_final: 0.8599 (tm-30) REVERT: G 30 LYS cc_start: 0.9267 (mtpp) cc_final: 0.8930 (mttp) REVERT: G 31 LYS cc_start: 0.8988 (tttm) cc_final: 0.8365 (tmtt) REVERT: G 50 ARG cc_start: 0.8906 (tpp-160) cc_final: 0.8339 (ttt90) REVERT: G 55 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8167 (tm-30) REVERT: G 58 LYS cc_start: 0.8860 (ttpm) cc_final: 0.8572 (tppt) REVERT: G 93 VAL cc_start: 0.8715 (t) cc_final: 0.8417 (m) REVERT: G 146 ARG cc_start: 0.8856 (ptp90) cc_final: 0.8282 (ptp90) REVERT: G 159 ARG cc_start: 0.8667 (ptt180) cc_final: 0.8382 (ttp80) REVERT: G 180 GLN cc_start: 0.8587 (mt0) cc_final: 0.8318 (mt0) REVERT: G 183 LEU cc_start: 0.9069 (mt) cc_final: 0.8695 (tt) REVERT: G 185 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8469 (tp40) REVERT: H 14 ARG cc_start: 0.8692 (mtt180) cc_final: 0.7827 (tpt170) REVERT: H 60 GLU cc_start: 0.7280 (pp20) cc_final: 0.6330 (mm-30) REVERT: H 90 MET cc_start: 0.8444 (mmp) cc_final: 0.7031 (ttt) REVERT: H 96 LYS cc_start: 0.9322 (tttp) cc_final: 0.9073 (ttpp) REVERT: H 97 THR cc_start: 0.8873 (m) cc_final: 0.8206 (p) outliers start: 3 outliers final: 1 residues processed: 1029 average time/residue: 0.6383 time to fit residues: 1009.4554 Evaluate side-chains 618 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 617 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 484 optimal weight: 50.0000 chunk 435 optimal weight: 50.0000 chunk 241 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 449 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 521 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 260 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 290 ASN B 316 GLN B 397 GLN B 477 GLN C 238 GLN C 283 HIS C 316 GLN C 459 GLN D 58 GLN D 161 ASN D 310 GLN E 129 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN F 344 HIS F 425 GLN G 3 GLN G 180 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39027 Z= 0.262 Angle : 0.643 14.361 53230 Z= 0.337 Chirality : 0.043 0.220 6273 Planarity : 0.005 0.064 7224 Dihedral : 6.202 161.564 6204 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.14 % Allowed : 4.03 % Favored : 95.83 % 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: -1.36 (0.11), residues: 5790 helix: 0.46 (0.09), residues: 3132 sheet: -2.10 (0.20), residues: 599 loop : -2.66 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 424 HIS 0.008 0.001 HIS C 418 PHE 0.038 0.002 PHE B 141 TYR 0.020 0.002 TYR E 263 ARG 0.010 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 753 time to evaluate : 4.874 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: 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 92 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8477 (tm-30) REVERT: A 96 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 102 ILE cc_start: 0.9029 (mt) cc_final: 0.8693 (tt) REVERT: A 196 GLN cc_start: 0.8860 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 257 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 311 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8735 (mt-10) REVERT: A 325 ASP cc_start: 0.7409 (p0) cc_final: 0.7099 (p0) REVERT: A 332 GLU cc_start: 0.8810 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 342 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8659 (mm-30) REVERT: A 459 GLN cc_start: 0.8822 (tp40) cc_final: 0.8432 (tp40) REVERT: A 478 ASP cc_start: 0.8622 (m-30) cc_final: 0.7922 (p0) REVERT: A 480 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8482 (mp0) REVERT: A 492 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8412 (tp30) REVERT: A 527 GLU cc_start: 0.8903 (pt0) cc_final: 0.8611 (tm-30) REVERT: B 41 ARG cc_start: 0.8881 (ttm170) cc_final: 0.8551 (ttm170) REVERT: B 60 VAL cc_start: 0.9208 (t) cc_final: 0.8700 (m) REVERT: B 133 MET cc_start: 0.8771 (ttt) cc_final: 0.7921 (mtp) REVERT: B 147 ILE cc_start: 0.8900 (mt) cc_final: 0.8689 (tt) REVERT: B 179 THR cc_start: 0.8299 (m) cc_final: 0.7611 (p) REVERT: B 251 VAL cc_start: 0.9602 (t) cc_final: 0.9362 (p) REVERT: B 261 GLU cc_start: 0.8794 (tt0) cc_final: 0.8478 (mt-10) REVERT: B 287 LEU cc_start: 0.8796 (tt) cc_final: 0.8546 (mp) REVERT: B 328 SER cc_start: 0.9464 (m) cc_final: 0.9004 (t) REVERT: B 336 GLU cc_start: 0.9087 (pm20) cc_final: 0.8767 (pm20) REVERT: B 342 GLU cc_start: 0.8990 (mp0) cc_final: 0.8727 (mp0) REVERT: B 343 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8294 (mm-30) REVERT: B 391 MET cc_start: 0.6983 (mmt) cc_final: 0.6304 (mmp) REVERT: B 416 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.8037 (mtm110) REVERT: B 417 ARG cc_start: 0.9107 (mtm110) cc_final: 0.8353 (tpt90) REVERT: B 480 GLU cc_start: 0.8560 (mp0) cc_final: 0.8077 (pm20) REVERT: B 481 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8262 (tpt-90) REVERT: B 541 GLN cc_start: 0.9160 (pt0) cc_final: 0.8720 (pm20) REVERT: B 546 GLU cc_start: 0.9196 (tt0) cc_final: 0.8687 (tm-30) REVERT: B 550 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8285 (ptt-90) REVERT: B 558 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8950 (tm-30) REVERT: C 3 GLN cc_start: 0.8464 (tt0) cc_final: 0.8263 (tm-30) REVERT: C 74 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8576 (tt0) REVERT: C 101 TYR cc_start: 0.8478 (m-80) cc_final: 0.8153 (m-80) REVERT: C 251 VAL cc_start: 0.9204 (t) cc_final: 0.8878 (m) REVERT: C 257 GLU cc_start: 0.7439 (tp30) cc_final: 0.7109 (tp30) REVERT: C 261 GLU cc_start: 0.9019 (mp0) cc_final: 0.8588 (mp0) REVERT: C 268 GLU cc_start: 0.9029 (pt0) cc_final: 0.8630 (tm-30) REVERT: C 282 MET cc_start: 0.8855 (tpt) cc_final: 0.8409 (tpp) REVERT: C 300 GLU cc_start: 0.9453 (tt0) cc_final: 0.9197 (tt0) REVERT: C 311 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8916 (mt-10) REVERT: C 410 ASP cc_start: 0.8103 (m-30) cc_final: 0.7640 (m-30) REVERT: C 456 GLU cc_start: 0.9014 (pp20) cc_final: 0.8382 (tp30) REVERT: C 538 GLU cc_start: 0.9466 (tt0) cc_final: 0.9235 (tm-30) REVERT: C 557 GLU cc_start: 0.8526 (pm20) cc_final: 0.8292 (pm20) REVERT: C 558 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7602 (mp0) REVERT: C 567 MET cc_start: 0.8212 (mtt) cc_final: 0.7771 (tpp) REVERT: D 62 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8465 (mm-30) REVERT: D 128 GLU cc_start: 0.7783 (pt0) cc_final: 0.7210 (mt-10) REVERT: D 129 GLN cc_start: 0.8802 (mt0) cc_final: 0.8213 (tm-30) REVERT: D 154 SER cc_start: 0.9065 (t) cc_final: 0.8653 (p) REVERT: D 206 GLN cc_start: 0.8878 (tt0) cc_final: 0.8675 (tp40) REVERT: D 237 MET cc_start: 0.8986 (mmt) cc_final: 0.8700 (mmm) REVERT: D 290 ASP cc_start: 0.9283 (t0) cc_final: 0.8591 (t0) REVERT: D 297 ARG cc_start: 0.8938 (mtp180) cc_final: 0.8715 (mtp85) REVERT: D 316 MET cc_start: 0.9007 (mtm) cc_final: 0.8772 (mtt) REVERT: D 333 THR cc_start: 0.9614 (p) cc_final: 0.9300 (t) REVERT: D 334 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8766 (mm-30) REVERT: D 338 GLN cc_start: 0.8937 (tt0) cc_final: 0.8235 (tp40) REVERT: D 364 ASN cc_start: 0.9298 (m110) cc_final: 0.8880 (t0) REVERT: D 374 ASP cc_start: 0.8753 (p0) cc_final: 0.8338 (p0) REVERT: D 420 ARG cc_start: 0.8926 (tmt170) cc_final: 0.8556 (ttp80) REVERT: D 425 GLN cc_start: 0.8520 (tt0) cc_final: 0.8170 (tt0) REVERT: D 445 MET cc_start: 0.9152 (mtp) cc_final: 0.8867 (ttt) REVERT: E 7 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9226 (mp0) REVERT: E 58 GLN cc_start: 0.9116 (tt0) cc_final: 0.8887 (tm-30) REVERT: E 206 GLN cc_start: 0.8904 (pp30) cc_final: 0.8320 (mm-40) REVERT: E 207 GLU cc_start: 0.9283 (tm-30) cc_final: 0.8327 (tm-30) REVERT: E 274 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8112 (ptm-80) REVERT: E 275 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8303 (tm-30) REVERT: E 280 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.7460 (tpp80) REVERT: E 295 TYR cc_start: 0.9066 (m-10) cc_final: 0.8808 (m-10) REVERT: E 316 MET cc_start: 0.8894 (mtm) cc_final: 0.8558 (mtm) REVERT: E 345 ARG cc_start: 0.9117 (mtm-85) cc_final: 0.8887 (mmm160) REVERT: E 364 ASN cc_start: 0.8279 (t0) cc_final: 0.8071 (t0) REVERT: E 401 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8680 (mp0) REVERT: E 437 GLN cc_start: 0.8852 (pt0) cc_final: 0.8345 (mm-40) REVERT: E 453 ARG cc_start: 0.8092 (mpt180) cc_final: 0.7736 (mtt90) REVERT: F 7 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9192 (mp0) REVERT: F 26 ASP cc_start: 0.9262 (m-30) cc_final: 0.8826 (t0) REVERT: F 53 GLU cc_start: 0.9413 (tt0) cc_final: 0.9122 (tt0) REVERT: F 60 PHE cc_start: 0.9235 (m-10) cc_final: 0.8372 (m-80) REVERT: F 61 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8238 (tm-30) REVERT: F 120 ASN cc_start: 0.9077 (t0) cc_final: 0.8590 (t0) REVERT: F 156 SER cc_start: 0.9040 (m) cc_final: 0.8696 (p) REVERT: F 170 GLN cc_start: 0.9150 (pm20) cc_final: 0.8584 (pp30) REVERT: F 207 GLU cc_start: 0.8756 (tp30) cc_final: 0.8533 (tm-30) REVERT: F 233 LEU cc_start: 0.9578 (mm) cc_final: 0.9369 (mt) REVERT: F 243 GLU cc_start: 0.8891 (pt0) cc_final: 0.8582 (pt0) REVERT: F 260 MET cc_start: 0.9055 (mmm) cc_final: 0.8681 (tpp) REVERT: F 305 LYS cc_start: 0.9463 (mmtp) cc_final: 0.9234 (ttmt) REVERT: F 342 GLU cc_start: 0.9396 (tt0) cc_final: 0.8857 (tp30) REVERT: F 416 ASP cc_start: 0.9030 (p0) cc_final: 0.8591 (t0) REVERT: F 419 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8188 (mt-10) REVERT: F 446 LEU cc_start: 0.9041 (mt) cc_final: 0.8777 (tp) REVERT: F 454 ILE cc_start: 0.8489 (mt) cc_final: 0.8159 (tt) REVERT: G 13 GLN cc_start: 0.9341 (tt0) cc_final: 0.8721 (tm-30) REVERT: G 30 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8880 (mttp) REVERT: G 31 LYS cc_start: 0.8996 (tttm) cc_final: 0.8780 (tttm) REVERT: G 153 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9012 (mm-30) REVERT: G 185 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8405 (tp-100) REVERT: H 14 ARG cc_start: 0.8885 (mtt180) cc_final: 0.7993 (mmm-85) REVERT: H 60 GLU cc_start: 0.7322 (pp20) cc_final: 0.6386 (mm-30) REVERT: H 95 ARG cc_start: 0.9282 (tpt90) cc_final: 0.8980 (mtm110) REVERT: H 96 LYS cc_start: 0.9420 (tttp) cc_final: 0.9143 (ttpp) REVERT: H 97 THR cc_start: 0.9181 (m) cc_final: 0.8458 (m) outliers start: 4 outliers final: 0 residues processed: 756 average time/residue: 0.5907 time to fit residues: 697.0536 Evaluate side-chains 578 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 4.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 433 optimal weight: 0.0060 chunk 354 optimal weight: 50.0000 chunk 143 optimal weight: 9.9990 chunk 522 optimal weight: 9.9990 chunk 564 optimal weight: 10.0000 chunk 465 optimal weight: 50.0000 chunk 517 optimal weight: 40.0000 chunk 178 optimal weight: 0.0870 chunk 418 optimal weight: 50.0000 overall best weight: 6.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 310 GLN E 428 GLN F 249 HIS F 425 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39027 Z= 0.252 Angle : 0.618 14.474 53230 Z= 0.320 Chirality : 0.043 0.222 6273 Planarity : 0.005 0.059 7224 Dihedral : 5.697 132.988 6204 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % 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: -0.44 (0.11), residues: 5790 helix: 1.35 (0.09), residues: 3128 sheet: -1.87 (0.21), residues: 570 loop : -2.44 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 330 HIS 0.006 0.001 HIS C 418 PHE 0.025 0.002 PHE B 141 TYR 0.017 0.002 TYR E 386 ARG 0.008 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 712 time to evaluate : 4.345 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 196 GLN cc_start: 0.8964 (tt0) cc_final: 0.8654 (tm-30) REVERT: A 257 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 325 ASP cc_start: 0.7496 (p0) cc_final: 0.7058 (p0) REVERT: A 332 GLU cc_start: 0.8781 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 342 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8710 (mm-30) REVERT: A 459 GLN cc_start: 0.8729 (tp40) cc_final: 0.8282 (tp40) REVERT: A 478 ASP cc_start: 0.8619 (m-30) cc_final: 0.7903 (p0) REVERT: A 480 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8316 (mp0) REVERT: A 492 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8349 (tp30) REVERT: A 527 GLU cc_start: 0.8887 (pt0) cc_final: 0.8607 (tm-30) REVERT: B 41 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8570 (ttm110) REVERT: B 133 MET cc_start: 0.8826 (ttt) cc_final: 0.7971 (mtp) REVERT: B 179 THR cc_start: 0.8614 (m) cc_final: 0.8043 (p) REVERT: B 251 VAL cc_start: 0.9633 (t) cc_final: 0.9407 (p) REVERT: B 261 GLU cc_start: 0.8894 (tt0) cc_final: 0.8562 (mt-10) REVERT: B 314 ARG cc_start: 0.8691 (ptt180) cc_final: 0.8412 (ptt-90) REVERT: B 328 SER cc_start: 0.9461 (m) cc_final: 0.9003 (t) REVERT: B 416 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8116 (mtm110) REVERT: B 417 ARG cc_start: 0.9091 (mtm110) cc_final: 0.8423 (tpt90) REVERT: B 480 GLU cc_start: 0.8489 (mp0) cc_final: 0.8006 (pm20) REVERT: B 481 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8137 (tpt-90) REVERT: B 541 GLN cc_start: 0.9169 (pt0) cc_final: 0.8718 (pm20) REVERT: B 546 GLU cc_start: 0.9149 (tt0) cc_final: 0.8558 (tm-30) REVERT: B 550 ARG cc_start: 0.8858 (mmt-90) cc_final: 0.8292 (ptt-90) REVERT: B 558 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8875 (tm-30) REVERT: C 26 ASP cc_start: 0.9154 (m-30) cc_final: 0.8896 (m-30) REVERT: C 74 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8674 (tt0) REVERT: C 81 ASN cc_start: 0.8594 (t0) cc_final: 0.8243 (t0) REVERT: C 89 ARG cc_start: 0.8924 (ptt180) cc_final: 0.8026 (ptp-110) REVERT: C 184 TYR cc_start: 0.8960 (p90) cc_final: 0.8484 (p90) REVERT: C 268 GLU cc_start: 0.9003 (pt0) cc_final: 0.8581 (tm-30) REVERT: C 282 MET cc_start: 0.8840 (tpt) cc_final: 0.8017 (tpt) REVERT: C 290 ASN cc_start: 0.8912 (t0) cc_final: 0.8169 (t0) REVERT: C 300 GLU cc_start: 0.9446 (tt0) cc_final: 0.9195 (tt0) REVERT: C 344 MET cc_start: 0.9058 (mmm) cc_final: 0.8670 (mmm) REVERT: C 410 ASP cc_start: 0.8165 (m-30) cc_final: 0.7721 (m-30) REVERT: C 456 GLU cc_start: 0.9018 (pp20) cc_final: 0.8334 (tp30) REVERT: C 538 GLU cc_start: 0.9475 (tt0) cc_final: 0.9228 (tm-30) REVERT: C 557 GLU cc_start: 0.8587 (pm20) cc_final: 0.8386 (pm20) REVERT: C 558 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7614 (mp0) REVERT: D 77 GLU cc_start: 0.8833 (tp30) cc_final: 0.8594 (tp30) REVERT: D 128 GLU cc_start: 0.7733 (pt0) cc_final: 0.7074 (mt-10) REVERT: D 129 GLN cc_start: 0.8730 (mt0) cc_final: 0.8381 (tm-30) REVERT: D 154 SER cc_start: 0.9086 (t) cc_final: 0.8712 (p) REVERT: D 206 GLN cc_start: 0.8869 (tt0) cc_final: 0.8655 (tp40) REVERT: D 237 MET cc_start: 0.9047 (mmt) cc_final: 0.8813 (mmm) REVERT: D 290 ASP cc_start: 0.9306 (t0) cc_final: 0.8752 (t0) REVERT: D 316 MET cc_start: 0.8980 (mtm) cc_final: 0.8747 (mtt) REVERT: D 333 THR cc_start: 0.9605 (p) cc_final: 0.9329 (t) REVERT: D 334 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8784 (mm-30) REVERT: D 338 GLN cc_start: 0.8890 (tt0) cc_final: 0.8248 (tp40) REVERT: D 364 ASN cc_start: 0.9291 (m110) cc_final: 0.8844 (t0) REVERT: D 374 ASP cc_start: 0.8672 (p0) cc_final: 0.8471 (p0) REVERT: D 420 ARG cc_start: 0.8918 (tmt170) cc_final: 0.8470 (ttp80) REVERT: D 425 GLN cc_start: 0.8526 (tt0) cc_final: 0.8251 (tt0) REVERT: E 7 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9261 (mp0) REVERT: E 58 GLN cc_start: 0.9140 (tt0) cc_final: 0.8908 (tm-30) REVERT: E 191 PHE cc_start: 0.9275 (t80) cc_final: 0.9039 (t80) REVERT: E 258 THR cc_start: 0.8613 (m) cc_final: 0.8316 (m) REVERT: E 274 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8097 (ptm-80) REVERT: E 275 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8308 (tm-30) REVERT: E 280 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7433 (tpp80) REVERT: E 345 ARG cc_start: 0.9149 (mtm-85) cc_final: 0.8918 (mmm160) REVERT: E 364 ASN cc_start: 0.8194 (t0) cc_final: 0.7973 (t0) REVERT: E 401 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8716 (mp0) REVERT: E 424 ASN cc_start: 0.9210 (t0) cc_final: 0.9002 (t0) REVERT: E 437 GLN cc_start: 0.8837 (pt0) cc_final: 0.8378 (mm-40) REVERT: E 453 ARG cc_start: 0.8066 (mpt180) cc_final: 0.7843 (mpt180) REVERT: F 7 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9189 (mp0) REVERT: F 26 ASP cc_start: 0.9270 (m-30) cc_final: 0.8861 (t0) REVERT: F 61 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8275 (tm-30) REVERT: F 120 ASN cc_start: 0.9053 (t0) cc_final: 0.8598 (t0) REVERT: F 156 SER cc_start: 0.8985 (m) cc_final: 0.8308 (p) REVERT: F 170 GLN cc_start: 0.9181 (pm20) cc_final: 0.8586 (pp30) REVERT: F 207 GLU cc_start: 0.8829 (tp30) cc_final: 0.8548 (tm-30) REVERT: F 281 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8534 (ttp-110) REVERT: F 342 GLU cc_start: 0.9354 (tt0) cc_final: 0.8808 (tp30) REVERT: F 446 LEU cc_start: 0.8921 (mt) cc_final: 0.8650 (tp) REVERT: G 19 ARG cc_start: 0.9162 (ttp-110) cc_final: 0.8638 (ptp-110) REVERT: G 22 GLN cc_start: 0.8821 (tp40) cc_final: 0.8415 (tm-30) REVERT: G 30 LYS cc_start: 0.9200 (mtpp) cc_final: 0.8889 (mttp) REVERT: G 50 ARG cc_start: 0.8889 (tpp-160) cc_final: 0.8389 (tpp80) REVERT: G 55 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7976 (tm-30) REVERT: G 144 GLU cc_start: 0.9146 (tp30) cc_final: 0.8743 (tp30) REVERT: G 153 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9084 (mm-30) REVERT: G 177 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8223 (mtm-85) REVERT: G 181 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8494 (mm-40) REVERT: G 185 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8276 (tp40) REVERT: H 14 ARG cc_start: 0.8884 (mtt180) cc_final: 0.7926 (mmm-85) REVERT: H 57 ARG cc_start: 0.8597 (mpt-90) cc_final: 0.8038 (mpt-90) REVERT: H 60 GLU cc_start: 0.7602 (pp20) cc_final: 0.6551 (mm-30) REVERT: H 95 ARG cc_start: 0.9281 (tpt90) cc_final: 0.9016 (mtm180) REVERT: H 97 THR cc_start: 0.9143 (m) cc_final: 0.8694 (p) outliers start: 1 outliers final: 0 residues processed: 713 average time/residue: 0.5717 time to fit residues: 636.2718 Evaluate side-chains 553 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 515 optimal weight: 40.0000 chunk 392 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 350 optimal weight: 50.0000 chunk 524 optimal weight: 8.9990 chunk 554 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 496 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 262 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 310 GLN F 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39027 Z= 0.204 Angle : 0.588 14.146 53230 Z= 0.301 Chirality : 0.043 0.240 6273 Planarity : 0.004 0.061 7224 Dihedral : 5.362 128.131 6204 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % 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: -0.01 (0.11), residues: 5790 helix: 1.75 (0.09), residues: 3129 sheet: -1.80 (0.21), residues: 574 loop : -2.32 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 440 HIS 0.005 0.001 HIS C 418 PHE 0.037 0.001 PHE C 269 TYR 0.034 0.001 TYR C 562 ARG 0.012 0.001 ARG G 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 706 time to evaluate : 4.356 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: 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 196 GLN cc_start: 0.8986 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 257 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 325 ASP cc_start: 0.7459 (p0) cc_final: 0.7018 (p0) REVERT: A 332 GLU cc_start: 0.8839 (tt0) cc_final: 0.8448 (tm-30) REVERT: A 342 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8676 (mm-30) REVERT: A 393 GLU cc_start: 0.8353 (mp0) cc_final: 0.8093 (mp0) REVERT: A 417 ARG cc_start: 0.8726 (mmt-90) cc_final: 0.8413 (mpt90) REVERT: A 459 GLN cc_start: 0.8631 (tp40) cc_final: 0.8203 (tp40) REVERT: A 478 ASP cc_start: 0.8604 (m-30) cc_final: 0.7765 (p0) REVERT: A 492 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8397 (tp30) REVERT: A 527 GLU cc_start: 0.8950 (pt0) cc_final: 0.8667 (tm-30) REVERT: B 19 MET cc_start: 0.9327 (mtm) cc_final: 0.9126 (mmp) REVERT: B 41 ARG cc_start: 0.8744 (ttm170) cc_final: 0.8522 (ttm110) REVERT: B 133 MET cc_start: 0.8832 (ttt) cc_final: 0.7991 (mtp) REVERT: B 166 TYR cc_start: 0.8379 (m-10) cc_final: 0.7779 (m-10) REVERT: B 179 THR cc_start: 0.8645 (m) cc_final: 0.8136 (p) REVERT: B 251 VAL cc_start: 0.9601 (t) cc_final: 0.9367 (p) REVERT: B 291 THR cc_start: 0.9057 (p) cc_final: 0.8819 (p) REVERT: B 328 SER cc_start: 0.9474 (m) cc_final: 0.9004 (t) REVERT: B 336 GLU cc_start: 0.8977 (mp0) cc_final: 0.8651 (mp0) REVERT: B 363 GLU cc_start: 0.9470 (tp30) cc_final: 0.8405 (tm-30) REVERT: B 416 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.8160 (mtm110) REVERT: B 417 ARG cc_start: 0.9109 (mtm110) cc_final: 0.8246 (tpt90) REVERT: B 480 GLU cc_start: 0.8270 (mp0) cc_final: 0.7889 (pm20) REVERT: B 481 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8096 (tpt-90) REVERT: B 541 GLN cc_start: 0.9143 (pt0) cc_final: 0.8691 (pm20) REVERT: B 546 GLU cc_start: 0.9165 (tt0) cc_final: 0.8691 (tm-30) REVERT: B 558 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8899 (tm-30) REVERT: C 24 MET cc_start: 0.8426 (tpp) cc_final: 0.8161 (tpp) REVERT: C 26 ASP cc_start: 0.9157 (m-30) cc_final: 0.8895 (m-30) REVERT: C 42 LEU cc_start: 0.8292 (mm) cc_final: 0.7989 (mm) REVERT: C 74 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8689 (tt0) REVERT: C 81 ASN cc_start: 0.8541 (t0) cc_final: 0.8340 (t0) REVERT: C 89 ARG cc_start: 0.8868 (ptt180) cc_final: 0.8012 (ptp-110) REVERT: C 154 ARG cc_start: 0.9198 (ttm110) cc_final: 0.8839 (ttm110) REVERT: C 184 TYR cc_start: 0.8957 (p90) cc_final: 0.8494 (p90) REVERT: C 268 GLU cc_start: 0.8930 (pt0) cc_final: 0.8582 (tm-30) REVERT: C 282 MET cc_start: 0.8745 (tpt) cc_final: 0.8298 (tpp) REVERT: C 300 GLU cc_start: 0.9438 (tt0) cc_final: 0.8951 (tm-30) REVERT: C 336 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9128 (tm-30) REVERT: C 344 MET cc_start: 0.8970 (mmm) cc_final: 0.8701 (mmm) REVERT: C 347 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8468 (mt-10) REVERT: C 410 ASP cc_start: 0.8163 (m-30) cc_final: 0.7699 (m-30) REVERT: C 456 GLU cc_start: 0.8971 (pp20) cc_final: 0.8324 (tp30) REVERT: C 538 GLU cc_start: 0.9460 (tt0) cc_final: 0.9219 (tm-30) REVERT: C 558 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7509 (mp0) REVERT: D 77 GLU cc_start: 0.8727 (tp30) cc_final: 0.8511 (tp30) REVERT: D 128 GLU cc_start: 0.7710 (pt0) cc_final: 0.7111 (mt-10) REVERT: D 129 GLN cc_start: 0.8595 (mt0) cc_final: 0.8279 (tm-30) REVERT: D 154 SER cc_start: 0.9100 (t) cc_final: 0.8767 (p) REVERT: D 197 THR cc_start: 0.7587 (m) cc_final: 0.7269 (p) REVERT: D 237 MET cc_start: 0.9061 (mmt) cc_final: 0.8523 (mmm) REVERT: D 290 ASP cc_start: 0.9222 (t0) cc_final: 0.8613 (t0) REVERT: D 333 THR cc_start: 0.9617 (p) cc_final: 0.9394 (t) REVERT: D 334 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9015 (mm-30) REVERT: D 338 GLN cc_start: 0.8845 (tt0) cc_final: 0.8258 (tp40) REVERT: D 364 ASN cc_start: 0.9277 (m110) cc_final: 0.8790 (t0) REVERT: D 374 ASP cc_start: 0.8811 (p0) cc_final: 0.8385 (p0) REVERT: D 420 ARG cc_start: 0.8945 (tmt170) cc_final: 0.8596 (ttp80) REVERT: D 425 GLN cc_start: 0.8418 (tt0) cc_final: 0.8080 (tt0) REVERT: E 58 GLN cc_start: 0.9127 (tt0) cc_final: 0.8903 (tm-30) REVERT: E 194 MET cc_start: 0.8361 (mtm) cc_final: 0.8127 (mtm) REVERT: E 258 THR cc_start: 0.8607 (m) cc_final: 0.8392 (m) REVERT: E 263 TYR cc_start: 0.9126 (t80) cc_final: 0.8908 (t80) REVERT: E 274 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8107 (ptm-80) REVERT: E 275 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8282 (tm-30) REVERT: E 316 MET cc_start: 0.8824 (mtp) cc_final: 0.8201 (ttm) REVERT: E 318 ASP cc_start: 0.8718 (t0) cc_final: 0.8409 (t0) REVERT: E 364 ASN cc_start: 0.8194 (t0) cc_final: 0.7903 (t0) REVERT: E 401 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8713 (mp0) REVERT: E 437 GLN cc_start: 0.8843 (pt0) cc_final: 0.8345 (mm-40) REVERT: E 453 ARG cc_start: 0.8066 (mpt180) cc_final: 0.7814 (mpt180) REVERT: F 7 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9051 (mp0) REVERT: F 26 ASP cc_start: 0.9264 (m-30) cc_final: 0.8894 (t0) REVERT: F 60 PHE cc_start: 0.9110 (m-10) cc_final: 0.8390 (m-80) REVERT: F 61 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8312 (tm-30) REVERT: F 156 SER cc_start: 0.8977 (m) cc_final: 0.8328 (p) REVERT: F 170 GLN cc_start: 0.9175 (pm20) cc_final: 0.8820 (pp30) REVERT: F 207 GLU cc_start: 0.8829 (tp30) cc_final: 0.8563 (tm-30) REVERT: F 260 MET cc_start: 0.8870 (mmp) cc_final: 0.8263 (mmp) REVERT: F 281 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8474 (ttm-80) REVERT: F 323 HIS cc_start: 0.8130 (t-90) cc_final: 0.7798 (t-90) REVERT: F 334 GLU cc_start: 0.8830 (pt0) cc_final: 0.8540 (pm20) REVERT: F 341 ARG cc_start: 0.9106 (mmm-85) cc_final: 0.8705 (mmm-85) REVERT: F 342 GLU cc_start: 0.9341 (tt0) cc_final: 0.8813 (tp30) REVERT: F 413 GLN cc_start: 0.8633 (mt0) cc_final: 0.8421 (mt0) REVERT: F 446 LEU cc_start: 0.8942 (mt) cc_final: 0.8707 (tp) REVERT: G 15 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8640 (tpp80) REVERT: G 22 GLN cc_start: 0.8721 (tp40) cc_final: 0.8267 (tm-30) REVERT: G 30 LYS cc_start: 0.9181 (mtpp) cc_final: 0.8840 (mttp) REVERT: G 55 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7947 (tm-30) REVERT: G 139 ARG cc_start: 0.9106 (tmm-80) cc_final: 0.8684 (tmm-80) REVERT: G 144 GLU cc_start: 0.9037 (tp30) cc_final: 0.8646 (tp30) REVERT: G 177 ARG cc_start: 0.8520 (ttp-110) cc_final: 0.8099 (mtm-85) REVERT: H 14 ARG cc_start: 0.8896 (mtt180) cc_final: 0.7911 (mmm-85) REVERT: H 57 ARG cc_start: 0.8652 (mpt-90) cc_final: 0.7950 (mpt-90) REVERT: H 60 GLU cc_start: 0.7455 (pp20) cc_final: 0.6601 (mm-30) REVERT: H 90 MET cc_start: 0.8252 (mmm) cc_final: 0.6812 (ttp) REVERT: H 95 ARG cc_start: 0.9354 (tpt90) cc_final: 0.8980 (mtt180) outliers start: 1 outliers final: 0 residues processed: 707 average time/residue: 0.5729 time to fit residues: 633.5083 Evaluate side-chains 539 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 462 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 8 optimal weight: 0.4980 chunk 413 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 473 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 283 optimal weight: 0.1980 chunk 498 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 425 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39027 Z= 0.249 Angle : 0.606 14.231 53230 Z= 0.311 Chirality : 0.043 0.246 6273 Planarity : 0.004 0.058 7224 Dihedral : 5.280 127.723 6204 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: 0.22 (0.12), residues: 5790 helix: 1.98 (0.09), residues: 3126 sheet: -1.75 (0.21), residues: 573 loop : -2.25 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 440 HIS 0.004 0.001 HIS E 252 PHE 0.018 0.002 PHE C 269 TYR 0.028 0.002 TYR C 562 ARG 0.019 0.001 ARG G 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 4.204 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: 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 196 GLN cc_start: 0.9027 (tt0) cc_final: 0.8688 (tm-30) REVERT: A 257 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7844 (mp0) REVERT: A 325 ASP cc_start: 0.7574 (p0) cc_final: 0.7201 (p0) REVERT: A 332 GLU cc_start: 0.8792 (tt0) cc_final: 0.8418 (tm-30) REVERT: A 342 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8657 (mm-30) REVERT: A 393 GLU cc_start: 0.8427 (mp0) cc_final: 0.8137 (mp0) REVERT: A 459 GLN cc_start: 0.8659 (tp40) cc_final: 0.8211 (tp40) REVERT: A 478 ASP cc_start: 0.8533 (m-30) cc_final: 0.7940 (p0) REVERT: A 480 GLU cc_start: 0.8731 (mp0) cc_final: 0.8030 (mp0) REVERT: A 492 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8461 (tp30) REVERT: A 527 GLU cc_start: 0.8942 (pt0) cc_final: 0.8684 (tm-30) REVERT: B 41 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8509 (ttm110) REVERT: B 133 MET cc_start: 0.8847 (ttt) cc_final: 0.8014 (mtp) REVERT: B 166 TYR cc_start: 0.8318 (m-10) cc_final: 0.7768 (m-10) REVERT: B 179 THR cc_start: 0.8684 (m) cc_final: 0.8233 (p) REVERT: B 251 VAL cc_start: 0.9628 (t) cc_final: 0.9401 (p) REVERT: B 328 SER cc_start: 0.9473 (m) cc_final: 0.9019 (t) REVERT: B 416 ARG cc_start: 0.8455 (ttp-110) cc_final: 0.8197 (mtm110) REVERT: B 417 ARG cc_start: 0.9125 (mtm110) cc_final: 0.8413 (tpt90) REVERT: B 456 GLU cc_start: 0.9239 (pp20) cc_final: 0.9022 (pp20) REVERT: B 459 GLN cc_start: 0.7681 (mp10) cc_final: 0.7352 (mp10) REVERT: B 480 GLU cc_start: 0.8355 (mp0) cc_final: 0.7897 (pm20) REVERT: B 481 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8153 (tpt-90) REVERT: B 541 GLN cc_start: 0.9068 (pt0) cc_final: 0.8791 (pm20) REVERT: B 546 GLU cc_start: 0.9144 (tt0) cc_final: 0.8658 (tm-30) REVERT: B 558 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8920 (tm-30) REVERT: C 24 MET cc_start: 0.8368 (tpp) cc_final: 0.8118 (tpp) REVERT: C 26 ASP cc_start: 0.9120 (m-30) cc_final: 0.8844 (m-30) REVERT: C 42 LEU cc_start: 0.8184 (mm) cc_final: 0.7923 (mm) REVERT: C 74 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8699 (tt0) REVERT: C 81 ASN cc_start: 0.8597 (t0) cc_final: 0.8390 (t0) REVERT: C 89 ARG cc_start: 0.8861 (ptt180) cc_final: 0.8616 (mtm180) REVERT: C 154 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8810 (ttm110) REVERT: C 184 TYR cc_start: 0.8963 (p90) cc_final: 0.8493 (p90) REVERT: C 268 GLU cc_start: 0.9003 (pt0) cc_final: 0.8566 (tm-30) REVERT: C 282 MET cc_start: 0.8741 (tpt) cc_final: 0.8317 (tpp) REVERT: C 300 GLU cc_start: 0.9409 (tt0) cc_final: 0.9030 (tm-30) REVERT: C 344 MET cc_start: 0.8977 (mmm) cc_final: 0.8704 (mmm) REVERT: C 347 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8548 (mt-10) REVERT: C 410 ASP cc_start: 0.8061 (m-30) cc_final: 0.7608 (m-30) REVERT: C 456 GLU cc_start: 0.8966 (pp20) cc_final: 0.8316 (tp30) REVERT: C 538 GLU cc_start: 0.9426 (tt0) cc_final: 0.9217 (tm-30) REVERT: C 558 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7427 (mp0) REVERT: D 128 GLU cc_start: 0.7715 (pt0) cc_final: 0.7111 (mt-10) REVERT: D 129 GLN cc_start: 0.8539 (mt0) cc_final: 0.8255 (tm-30) REVERT: D 154 SER cc_start: 0.9162 (t) cc_final: 0.8828 (p) REVERT: D 237 MET cc_start: 0.9046 (mmt) cc_final: 0.8642 (mmm) REVERT: D 290 ASP cc_start: 0.9268 (t0) cc_final: 0.8673 (t0) REVERT: D 333 THR cc_start: 0.9599 (p) cc_final: 0.9355 (t) REVERT: D 334 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9048 (mm-30) REVERT: D 338 GLN cc_start: 0.8846 (tt0) cc_final: 0.8242 (tp40) REVERT: D 364 ASN cc_start: 0.9285 (m110) cc_final: 0.8820 (t0) REVERT: D 374 ASP cc_start: 0.8699 (p0) cc_final: 0.8280 (p0) REVERT: D 420 ARG cc_start: 0.8911 (tmt170) cc_final: 0.8442 (ttp80) REVERT: D 425 GLN cc_start: 0.8435 (tt0) cc_final: 0.8187 (tt0) REVERT: E 58 GLN cc_start: 0.9121 (tt0) cc_final: 0.8894 (tm-30) REVERT: E 120 ASN cc_start: 0.9267 (t0) cc_final: 0.9054 (t0) REVERT: E 223 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8503 (tptp) REVERT: E 258 THR cc_start: 0.8774 (m) cc_final: 0.8536 (m) REVERT: E 259 ASP cc_start: 0.8708 (t0) cc_final: 0.8500 (t0) REVERT: E 274 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8082 (ptm-80) REVERT: E 275 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8293 (tm-30) REVERT: E 316 MET cc_start: 0.8915 (mtp) cc_final: 0.8318 (ttm) REVERT: E 318 ASP cc_start: 0.8767 (t0) cc_final: 0.8381 (t0) REVERT: E 334 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8518 (mm-30) REVERT: E 364 ASN cc_start: 0.8298 (t0) cc_final: 0.7998 (t0) REVERT: E 401 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8716 (mp0) REVERT: E 437 GLN cc_start: 0.8843 (pt0) cc_final: 0.8418 (mm-40) REVERT: E 461 LYS cc_start: 0.8936 (pttm) cc_final: 0.8540 (pttm) REVERT: F 26 ASP cc_start: 0.9300 (m-30) cc_final: 0.8902 (t0) REVERT: F 60 PHE cc_start: 0.9107 (m-10) cc_final: 0.8342 (m-80) REVERT: F 61 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8307 (tm-30) REVERT: F 156 SER cc_start: 0.9002 (m) cc_final: 0.8667 (p) REVERT: F 170 GLN cc_start: 0.9143 (pm20) cc_final: 0.8506 (pp30) REVERT: F 207 GLU cc_start: 0.8820 (tp30) cc_final: 0.8547 (tm-30) REVERT: F 260 MET cc_start: 0.8947 (mmp) cc_final: 0.8635 (mmp) REVERT: F 281 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8430 (ttm-80) REVERT: F 323 HIS cc_start: 0.8219 (t-90) cc_final: 0.7964 (t-90) REVERT: F 342 GLU cc_start: 0.9332 (tt0) cc_final: 0.8817 (tp30) REVERT: F 446 LEU cc_start: 0.8909 (mt) cc_final: 0.8679 (tp) REVERT: G 19 ARG cc_start: 0.9173 (ttp-110) cc_final: 0.8723 (ptp-110) REVERT: G 22 GLN cc_start: 0.8737 (tp40) cc_final: 0.8285 (tm-30) REVERT: G 30 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8753 (mttp) REVERT: G 144 GLU cc_start: 0.9000 (tp30) cc_final: 0.8761 (tp30) REVERT: G 183 LEU cc_start: 0.9102 (mt) cc_final: 0.8719 (tt) REVERT: G 185 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8196 (tp40) REVERT: H 14 ARG cc_start: 0.8927 (mtt180) cc_final: 0.7969 (mmm-85) REVERT: H 57 ARG cc_start: 0.8812 (mpt-90) cc_final: 0.7894 (ptt-90) REVERT: H 60 GLU cc_start: 0.7719 (pp20) cc_final: 0.6664 (mm-30) REVERT: H 90 MET cc_start: 0.8113 (mmm) cc_final: 0.6953 (ttp) REVERT: H 95 ARG cc_start: 0.9391 (tpt90) cc_final: 0.9003 (mtt180) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.5687 time to fit residues: 599.6429 Evaluate side-chains 534 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 534 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 186 optimal weight: 0.0050 chunk 499 optimal weight: 50.0000 chunk 109 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 555 optimal weight: 10.0000 chunk 461 optimal weight: 50.0000 chunk 257 optimal weight: 0.0980 chunk 46 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 overall best weight: 4.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN F 425 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39027 Z= 0.190 Angle : 0.571 13.142 53230 Z= 0.292 Chirality : 0.043 0.250 6273 Planarity : 0.004 0.056 7224 Dihedral : 5.077 125.212 6204 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 0.41 (0.12), residues: 5790 helix: 2.14 (0.09), residues: 3120 sheet: -1.63 (0.22), residues: 557 loop : -2.17 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 440 HIS 0.004 0.001 HIS C 418 PHE 0.015 0.001 PHE A 559 TYR 0.026 0.001 TYR C 562 ARG 0.008 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 4.380 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.9016 (tt0) cc_final: 0.8688 (tm-30) REVERT: A 257 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7818 (mp0) REVERT: A 325 ASP cc_start: 0.7485 (p0) cc_final: 0.7056 (p0) REVERT: A 332 GLU cc_start: 0.8892 (tt0) cc_final: 0.8433 (tm-30) REVERT: A 342 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8622 (mm-30) REVERT: A 393 GLU cc_start: 0.8406 (mp0) cc_final: 0.8107 (mp0) REVERT: A 417 ARG cc_start: 0.8714 (mmt-90) cc_final: 0.8279 (mpt90) REVERT: A 459 GLN cc_start: 0.8553 (tp40) cc_final: 0.8117 (tp40) REVERT: A 478 ASP cc_start: 0.8504 (m-30) cc_final: 0.7875 (p0) REVERT: A 480 GLU cc_start: 0.8726 (mp0) cc_final: 0.8086 (mp0) REVERT: A 492 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8463 (tp30) REVERT: A 527 GLU cc_start: 0.8946 (pt0) cc_final: 0.8706 (tm-30) REVERT: B 19 MET cc_start: 0.9345 (mtm) cc_final: 0.9140 (mmp) REVERT: B 41 ARG cc_start: 0.8808 (ttm170) cc_final: 0.8500 (ttm110) REVERT: B 133 MET cc_start: 0.8860 (ttt) cc_final: 0.8016 (mtp) REVERT: B 166 TYR cc_start: 0.8340 (m-10) cc_final: 0.7930 (m-10) REVERT: B 179 THR cc_start: 0.8778 (m) cc_final: 0.8346 (p) REVERT: B 251 VAL cc_start: 0.9632 (t) cc_final: 0.9430 (p) REVERT: B 328 SER cc_start: 0.9475 (m) cc_final: 0.9040 (t) REVERT: B 336 GLU cc_start: 0.8969 (mp0) cc_final: 0.8664 (mp0) REVERT: B 416 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8218 (mtm110) REVERT: B 417 ARG cc_start: 0.9147 (mtm110) cc_final: 0.8447 (tpt90) REVERT: B 480 GLU cc_start: 0.8260 (mp0) cc_final: 0.7867 (pm20) REVERT: B 481 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8117 (tpt-90) REVERT: B 541 GLN cc_start: 0.9111 (pt0) cc_final: 0.8583 (pm20) REVERT: B 546 GLU cc_start: 0.9114 (tt0) cc_final: 0.8620 (tm-30) REVERT: B 558 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8865 (tm-30) REVERT: C 26 ASP cc_start: 0.9131 (m-30) cc_final: 0.8836 (m-30) REVERT: C 74 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8694 (tt0) REVERT: C 81 ASN cc_start: 0.8545 (t0) cc_final: 0.8281 (t0) REVERT: C 89 ARG cc_start: 0.8873 (ptt180) cc_final: 0.8661 (mtm180) REVERT: C 93 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7982 (mmm-85) REVERT: C 154 ARG cc_start: 0.9164 (ttm110) cc_final: 0.8810 (ttm110) REVERT: C 184 TYR cc_start: 0.8945 (p90) cc_final: 0.8503 (p90) REVERT: C 268 GLU cc_start: 0.9038 (pt0) cc_final: 0.8350 (tp30) REVERT: C 282 MET cc_start: 0.8749 (tpt) cc_final: 0.8306 (tpp) REVERT: C 300 GLU cc_start: 0.9382 (tt0) cc_final: 0.9073 (tm-30) REVERT: C 344 MET cc_start: 0.9015 (mmm) cc_final: 0.8812 (mmm) REVERT: C 410 ASP cc_start: 0.8042 (m-30) cc_final: 0.7591 (m-30) REVERT: C 456 GLU cc_start: 0.8956 (pp20) cc_final: 0.8305 (tp30) REVERT: C 516 MET cc_start: 0.8650 (ttt) cc_final: 0.8241 (tmm) REVERT: C 538 GLU cc_start: 0.9407 (tt0) cc_final: 0.9191 (tm-30) REVERT: D 128 GLU cc_start: 0.7601 (pt0) cc_final: 0.6997 (mt-10) REVERT: D 129 GLN cc_start: 0.8431 (mt0) cc_final: 0.8164 (tm-30) REVERT: D 154 SER cc_start: 0.9129 (t) cc_final: 0.8843 (p) REVERT: D 237 MET cc_start: 0.8964 (mmt) cc_final: 0.8648 (mmm) REVERT: D 290 ASP cc_start: 0.9195 (t0) cc_final: 0.8584 (t0) REVERT: D 333 THR cc_start: 0.9565 (p) cc_final: 0.9322 (t) REVERT: D 334 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9082 (mm-30) REVERT: D 338 GLN cc_start: 0.8826 (tt0) cc_final: 0.8243 (tp40) REVERT: D 364 ASN cc_start: 0.9286 (m110) cc_final: 0.8803 (t0) REVERT: D 374 ASP cc_start: 0.8661 (p0) cc_final: 0.8139 (p0) REVERT: D 408 ASP cc_start: 0.8265 (m-30) cc_final: 0.7920 (m-30) REVERT: D 420 ARG cc_start: 0.8906 (tmt170) cc_final: 0.8423 (ttp80) REVERT: D 425 GLN cc_start: 0.8283 (tt0) cc_final: 0.8068 (tt0) REVERT: D 445 MET cc_start: 0.9017 (ttt) cc_final: 0.8733 (ttt) REVERT: E 58 GLN cc_start: 0.9127 (tt0) cc_final: 0.8893 (tm-30) REVERT: E 120 ASN cc_start: 0.9238 (t0) cc_final: 0.9029 (t0) REVERT: E 258 THR cc_start: 0.8767 (m) cc_final: 0.8509 (m) REVERT: E 259 ASP cc_start: 0.8649 (t0) cc_final: 0.8431 (t0) REVERT: E 274 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8050 (ptm-80) REVERT: E 275 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8281 (tm-30) REVERT: E 334 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8523 (mm-30) REVERT: E 364 ASN cc_start: 0.8183 (t0) cc_final: 0.7879 (t0) REVERT: E 401 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8728 (mp0) REVERT: E 437 GLN cc_start: 0.8863 (pt0) cc_final: 0.8487 (mm-40) REVERT: E 461 LYS cc_start: 0.8948 (pttm) cc_final: 0.8573 (pttm) REVERT: F 26 ASP cc_start: 0.9283 (m-30) cc_final: 0.8893 (t0) REVERT: F 60 PHE cc_start: 0.9056 (m-10) cc_final: 0.8014 (m-80) REVERT: F 61 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8305 (tm-30) REVERT: F 156 SER cc_start: 0.8986 (m) cc_final: 0.8653 (p) REVERT: F 170 GLN cc_start: 0.9193 (pm20) cc_final: 0.8621 (pp30) REVERT: F 172 THR cc_start: 0.8730 (p) cc_final: 0.8516 (t) REVERT: F 207 GLU cc_start: 0.8831 (tp30) cc_final: 0.8535 (tm-30) REVERT: F 260 MET cc_start: 0.9081 (mmp) cc_final: 0.8849 (mmp) REVERT: F 342 GLU cc_start: 0.9319 (tt0) cc_final: 0.8779 (tp30) REVERT: F 419 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8331 (mt-10) REVERT: G 19 ARG cc_start: 0.9178 (ttp-110) cc_final: 0.8640 (ptp-110) REVERT: G 22 GLN cc_start: 0.8766 (tp40) cc_final: 0.8309 (tm-30) REVERT: G 30 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8940 (mmtp) REVERT: G 144 GLU cc_start: 0.8985 (tp30) cc_final: 0.8700 (tp30) REVERT: G 153 GLU cc_start: 0.9384 (tp30) cc_final: 0.9158 (mm-30) REVERT: G 177 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8096 (mtm-85) REVERT: G 183 LEU cc_start: 0.9105 (mt) cc_final: 0.8736 (tt) REVERT: H 14 ARG cc_start: 0.8980 (mtt180) cc_final: 0.7985 (mmm-85) REVERT: H 60 GLU cc_start: 0.7626 (pp20) cc_final: 0.6733 (mm-30) REVERT: H 90 MET cc_start: 0.8116 (mmm) cc_final: 0.7104 (ttp) REVERT: H 95 ARG cc_start: 0.9408 (tpt90) cc_final: 0.9002 (mtt90) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.5586 time to fit residues: 605.6115 Evaluate side-chains 540 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 316 optimal weight: 9.9990 chunk 405 optimal weight: 9.9990 chunk 314 optimal weight: 20.0000 chunk 467 optimal weight: 50.0000 chunk 310 optimal weight: 7.9990 chunk 553 optimal weight: 40.0000 chunk 346 optimal weight: 20.0000 chunk 337 optimal weight: 40.0000 chunk 255 optimal weight: 20.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 39027 Z= 0.429 Angle : 0.733 16.966 53230 Z= 0.380 Chirality : 0.047 0.352 6273 Planarity : 0.005 0.080 7224 Dihedral : 5.477 108.687 6204 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 0.29 (0.12), residues: 5790 helix: 2.05 (0.09), residues: 3135 sheet: -1.82 (0.22), residues: 541 loop : -2.24 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 97 HIS 0.009 0.002 HIS E 252 PHE 0.038 0.002 PHE C 269 TYR 0.037 0.002 TYR F 383 ARG 0.010 0.001 ARG E 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 4.348 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.9015 (tt0) cc_final: 0.8694 (tm-30) REVERT: A 257 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7737 (mp0) REVERT: A 325 ASP cc_start: 0.7619 (p0) cc_final: 0.7353 (p0) REVERT: A 332 GLU cc_start: 0.8907 (tt0) cc_final: 0.8303 (tm-30) REVERT: A 336 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 342 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8596 (mm-30) REVERT: A 424 TRP cc_start: 0.7876 (t60) cc_final: 0.7413 (t60) REVERT: A 459 GLN cc_start: 0.8699 (tp40) cc_final: 0.8441 (tp40) REVERT: A 478 ASP cc_start: 0.8591 (m-30) cc_final: 0.7969 (p0) REVERT: A 480 GLU cc_start: 0.8847 (mp0) cc_final: 0.8190 (mp0) REVERT: A 492 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8663 (tp30) REVERT: A 527 GLU cc_start: 0.8967 (pt0) cc_final: 0.8751 (tm-30) REVERT: B 19 MET cc_start: 0.9390 (mtm) cc_final: 0.9161 (mmp) REVERT: B 41 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8634 (ttm110) REVERT: B 133 MET cc_start: 0.8960 (ttt) cc_final: 0.8130 (mtp) REVERT: B 166 TYR cc_start: 0.8370 (m-10) cc_final: 0.7820 (m-10) REVERT: B 179 THR cc_start: 0.8917 (m) cc_final: 0.8560 (p) REVERT: B 251 VAL cc_start: 0.9646 (t) cc_final: 0.9445 (p) REVERT: B 328 SER cc_start: 0.9516 (m) cc_final: 0.9095 (t) REVERT: B 336 GLU cc_start: 0.8955 (mp0) cc_final: 0.8637 (mp0) REVERT: B 363 GLU cc_start: 0.9444 (tp30) cc_final: 0.8873 (tm-30) REVERT: B 391 MET cc_start: 0.6551 (mmt) cc_final: 0.6342 (mmp) REVERT: B 416 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8091 (mtm110) REVERT: B 417 ARG cc_start: 0.9132 (mtm110) cc_final: 0.8283 (tpt90) REVERT: B 459 GLN cc_start: 0.7822 (mp10) cc_final: 0.7539 (mp10) REVERT: B 480 GLU cc_start: 0.8537 (mp0) cc_final: 0.8047 (pm20) REVERT: B 481 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8156 (tpt-90) REVERT: B 541 GLN cc_start: 0.9062 (pt0) cc_final: 0.8637 (pm20) REVERT: B 546 GLU cc_start: 0.9135 (tt0) cc_final: 0.8706 (tm-30) REVERT: B 550 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8447 (ptt-90) REVERT: B 558 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8927 (tm-30) REVERT: C 74 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8595 (tt0) REVERT: C 89 ARG cc_start: 0.8807 (ptt180) cc_final: 0.8556 (mtm180) REVERT: C 154 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8802 (ttm110) REVERT: C 268 GLU cc_start: 0.9134 (pt0) cc_final: 0.8735 (tm-30) REVERT: C 282 MET cc_start: 0.8843 (tpt) cc_final: 0.8454 (tpp) REVERT: C 290 ASN cc_start: 0.8678 (t0) cc_final: 0.8474 (t0) REVERT: C 300 GLU cc_start: 0.9338 (tt0) cc_final: 0.9086 (tm-30) REVERT: C 344 MET cc_start: 0.9039 (mmm) cc_final: 0.8781 (mmm) REVERT: C 410 ASP cc_start: 0.7900 (m-30) cc_final: 0.7471 (m-30) REVERT: C 416 ARG cc_start: 0.9162 (mpp80) cc_final: 0.8610 (mpp80) REVERT: C 456 GLU cc_start: 0.9054 (pp20) cc_final: 0.8414 (tp30) REVERT: C 477 GLN cc_start: 0.7218 (mp10) cc_final: 0.6999 (mm-40) REVERT: C 516 MET cc_start: 0.8693 (ttt) cc_final: 0.8216 (tmm) REVERT: C 538 GLU cc_start: 0.9420 (tt0) cc_final: 0.9215 (tm-30) REVERT: D 77 GLU cc_start: 0.8794 (tp30) cc_final: 0.8556 (tp30) REVERT: D 88 MET cc_start: 0.8944 (ptm) cc_final: 0.8696 (ptm) REVERT: D 128 GLU cc_start: 0.8063 (pt0) cc_final: 0.7635 (mt-10) REVERT: D 129 GLN cc_start: 0.8641 (mt0) cc_final: 0.8375 (tm-30) REVERT: D 154 SER cc_start: 0.9059 (t) cc_final: 0.8746 (p) REVERT: D 237 MET cc_start: 0.9029 (mmt) cc_final: 0.8665 (mmm) REVERT: D 286 TYR cc_start: 0.8919 (p90) cc_final: 0.8692 (p90) REVERT: D 290 ASP cc_start: 0.9324 (t0) cc_final: 0.8931 (t0) REVERT: D 333 THR cc_start: 0.9527 (p) cc_final: 0.9288 (t) REVERT: D 334 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9035 (mm-30) REVERT: D 338 GLN cc_start: 0.8866 (tt0) cc_final: 0.8181 (tp40) REVERT: D 364 ASN cc_start: 0.9323 (m110) cc_final: 0.8863 (t0) REVERT: D 420 ARG cc_start: 0.8951 (tmt170) cc_final: 0.8194 (tmt-80) REVERT: D 425 GLN cc_start: 0.8257 (tt0) cc_final: 0.8022 (tt0) REVERT: E 58 GLN cc_start: 0.9126 (tt0) cc_final: 0.8855 (tm-30) REVERT: E 120 ASN cc_start: 0.9288 (t0) cc_final: 0.9071 (t0) REVERT: E 141 MET cc_start: 0.8439 (ptp) cc_final: 0.8076 (ptp) REVERT: E 259 ASP cc_start: 0.8802 (t0) cc_final: 0.8570 (t0) REVERT: E 274 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8008 (ptm-80) REVERT: E 275 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8246 (tm-30) REVERT: E 316 MET cc_start: 0.9094 (mtp) cc_final: 0.8894 (mtm) REVERT: E 321 ARG cc_start: 0.8150 (mtm110) cc_final: 0.7873 (mtm110) REVERT: E 334 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8484 (mm-30) REVERT: E 364 ASN cc_start: 0.8520 (t0) cc_final: 0.8143 (t0) REVERT: E 401 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8717 (mp0) REVERT: E 437 GLN cc_start: 0.8886 (pt0) cc_final: 0.8464 (mm110) REVERT: E 461 LYS cc_start: 0.8960 (pttm) cc_final: 0.8626 (pttm) REVERT: F 26 ASP cc_start: 0.9282 (m-30) cc_final: 0.8924 (t0) REVERT: F 141 MET cc_start: 0.8453 (mtp) cc_final: 0.8146 (mtp) REVERT: F 156 SER cc_start: 0.9033 (m) cc_final: 0.8411 (p) REVERT: F 207 GLU cc_start: 0.9026 (tp30) cc_final: 0.8627 (tm-30) REVERT: F 260 MET cc_start: 0.9076 (mmp) cc_final: 0.8483 (mmp) REVERT: F 281 ARG cc_start: 0.8814 (mtm180) cc_final: 0.8503 (mtm-85) REVERT: F 342 GLU cc_start: 0.9335 (tt0) cc_final: 0.8818 (tp30) REVERT: F 362 MET cc_start: 0.9136 (ptm) cc_final: 0.8844 (ptm) REVERT: F 462 TYR cc_start: 0.8652 (m-10) cc_final: 0.8430 (m-10) REVERT: G 22 GLN cc_start: 0.8749 (tp40) cc_final: 0.8285 (tm-30) REVERT: G 30 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8937 (mmtp) REVERT: G 144 GLU cc_start: 0.9044 (tp30) cc_final: 0.8820 (tp30) REVERT: G 177 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8100 (mtm-85) REVERT: G 183 LEU cc_start: 0.9140 (mt) cc_final: 0.8787 (tt) REVERT: G 185 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8310 (tp-100) REVERT: H 14 ARG cc_start: 0.8935 (mtt180) cc_final: 0.7898 (mmm-85) REVERT: H 28 GLU cc_start: 0.7774 (pt0) cc_final: 0.7085 (pm20) REVERT: H 60 GLU cc_start: 0.7541 (pp20) cc_final: 0.6719 (mm-30) REVERT: H 90 MET cc_start: 0.8338 (mmm) cc_final: 0.7234 (ttp) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.6146 time to fit residues: 611.5435 Evaluate side-chains 506 residues out of total 4575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 342 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 330 optimal weight: 30.0000 chunk 166 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 351 optimal weight: 50.0000 chunk 376 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 434 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: