Starting phenix.real_space_refine on Wed Feb 14 00:19:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/02_2024/6q6i_4468_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/02_2024/6q6i_4468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/02_2024/6q6i_4468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/02_2024/6q6i_4468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/02_2024/6q6i_4468_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6i_4468/02_2024/6q6i_4468_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 230 5.16 5 C 36400 2.51 5 N 9990 2.21 5 O 10570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "B ARG 721": "NH1" <-> "NH2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "C GLU 714": "OE1" <-> "OE2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D ARG 721": "NH1" <-> "NH2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E GLU 339": "OE1" <-> "OE2" Residue "E GLU 447": "OE1" <-> "OE2" Residue "E GLU 518": "OE1" <-> "OE2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E GLU 557": "OE1" <-> "OE2" Residue "E GLU 714": "OE1" <-> "OE2" Residue "E ARG 721": "NH1" <-> "NH2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "F GLU 557": "OE1" <-> "OE2" Residue "F GLU 714": "OE1" <-> "OE2" Residue "F ARG 721": "NH1" <-> "NH2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 339": "OE1" <-> "OE2" Residue "G GLU 447": "OE1" <-> "OE2" Residue "G GLU 518": "OE1" <-> "OE2" Residue "G ARG 553": "NH1" <-> "NH2" Residue "G GLU 557": "OE1" <-> "OE2" Residue "G GLU 714": "OE1" <-> "OE2" Residue "G ARG 721": "NH1" <-> "NH2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H GLU 339": "OE1" <-> "OE2" Residue "H GLU 447": "OE1" <-> "OE2" Residue "H GLU 518": "OE1" <-> "OE2" Residue "H ARG 553": "NH1" <-> "NH2" Residue "H GLU 557": "OE1" <-> "OE2" Residue "H GLU 714": "OE1" <-> "OE2" Residue "H ARG 721": "NH1" <-> "NH2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 192": "OE1" <-> "OE2" Residue "I ARG 196": "NH1" <-> "NH2" Residue "I ARG 253": "NH1" <-> "NH2" Residue "I GLU 339": "OE1" <-> "OE2" Residue "I GLU 447": "OE1" <-> "OE2" Residue "I GLU 518": "OE1" <-> "OE2" Residue "I ARG 553": "NH1" <-> "NH2" Residue "I GLU 557": "OE1" <-> "OE2" Residue "I GLU 714": "OE1" <-> "OE2" Residue "I ARG 721": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J GLU 192": "OE1" <-> "OE2" Residue "J ARG 196": "NH1" <-> "NH2" Residue "J ARG 253": "NH1" <-> "NH2" Residue "J GLU 339": "OE1" <-> "OE2" Residue "J GLU 447": "OE1" <-> "OE2" Residue "J GLU 518": "OE1" <-> "OE2" Residue "J ARG 553": "NH1" <-> "NH2" Residue "J GLU 557": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J ARG 721": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57200 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS A 750 " pdbres="PLP A 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS B 750 " pdbres="PLP B 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS C 750 " pdbres="PLP C 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS D 750 " pdbres="PLP D 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS E 750 " pdbres="PLP E 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS F 750 " pdbres="PLP F 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS G 750 " pdbres="PLP G 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS H 750 " pdbres="PLP H 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS I 750 " pdbres="PLP I 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5720 Unusual residues: {'PLP': 1} Classifications: {'peptide': 749, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 711, None: 1} Not linked: pdbres="LYS J 750 " pdbres="PLP J 801 " Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Time building chain proxies: 21.94, per 1000 atoms: 0.38 Number of scatterers: 57200 At special positions: 0 Unit cell: (189.198, 193.275, 103.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 10 15.00 O 10570 8.00 N 9990 7.00 C 36400 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.81 Conformation dependent library (CDL) restraints added in 8.1 seconds 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 280 helices and 50 sheets defined 29.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 129 through 146 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA A 217 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 Processing helix chain 'A' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY A 451 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER A 453 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 455 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A 456 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 459 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 461 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 603 through 606 No H-bonds generated for 'chain 'A' and resid 603 through 606' Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 647 " --> pdb=" O MET A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU A 714 " --> pdb=" O ASP A 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 717 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 718 " --> pdb=" O PHE A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 719 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 721 " --> pdb=" O THR A 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 722 " --> pdb=" O PHE A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 129 through 146 Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA B 217 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY B 451 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B 453 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 455 " --> pdb=" O ARG B 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN B 456 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 461 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.696A pdb=" N SER B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 557 " --> pdb=" O ARG B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 603 through 606 No H-bonds generated for 'chain 'B' and resid 603 through 606' Processing helix chain 'B' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 647 " --> pdb=" O MET B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 665 No H-bonds generated for 'chain 'B' and resid 662 through 665' Processing helix chain 'B' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU B 714 " --> pdb=" O ASP B 711 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 717 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 718 " --> pdb=" O PHE B 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 719 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 721 " --> pdb=" O THR B 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 722 " --> pdb=" O PHE B 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 52 No H-bonds generated for 'chain 'C' and resid 49 through 52' Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 129 through 146 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA C 217 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 420 through 426 removed outlier: 5.401A pdb=" N MET C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY C 451 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER C 453 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE C 455 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN C 456 " --> pdb=" O SER C 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 459 " --> pdb=" O GLN C 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 461 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER C 552 " --> pdb=" O ALA C 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 603 through 606 No H-bonds generated for 'chain 'C' and resid 603 through 606' Processing helix chain 'C' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA C 632 " --> pdb=" O ASP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 647 " --> pdb=" O MET C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 665 No H-bonds generated for 'chain 'C' and resid 662 through 665' Processing helix chain 'C' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU C 714 " --> pdb=" O ASP C 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 717 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 718 " --> pdb=" O PHE C 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 719 " --> pdb=" O ALA C 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 721 " --> pdb=" O THR C 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 722 " --> pdb=" O PHE C 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 129 through 146 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 214 through 219 removed outlier: 3.629A pdb=" N ALA D 217 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 441 Processing helix chain 'D' and resid 448 through 462 removed outlier: 4.032A pdb=" N GLY D 451 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D 452 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER D 453 " --> pdb=" O ALA D 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 455 " --> pdb=" O ARG D 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN D 456 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 459 " --> pdb=" O GLN D 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 461 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA D 470 " --> pdb=" O ARG D 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER D 552 " --> pdb=" O ALA D 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 557 " --> pdb=" O ARG D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 591 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 603 through 606 No H-bonds generated for 'chain 'D' and resid 603 through 606' Processing helix chain 'D' and resid 623 through 633 removed outlier: 3.634A pdb=" N ALA D 632 " --> pdb=" O ASP D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 647 " --> pdb=" O MET D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 665 No H-bonds generated for 'chain 'D' and resid 662 through 665' Processing helix chain 'D' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU D 714 " --> pdb=" O ASP D 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 717 " --> pdb=" O GLU D 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 718 " --> pdb=" O PHE D 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 719 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 721 " --> pdb=" O THR D 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 722 " --> pdb=" O PHE D 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 52 No H-bonds generated for 'chain 'E' and resid 49 through 52' Processing helix chain 'E' and resid 76 through 86 Processing helix chain 'E' and resid 129 through 146 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA E 217 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 239 through 248 removed outlier: 4.386A pdb=" N LYS E 244 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA E 309 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 441 Processing helix chain 'E' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY E 451 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG E 452 " --> pdb=" O PRO E 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER E 453 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 455 " --> pdb=" O ARG E 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN E 456 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 459 " --> pdb=" O GLN E 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 461 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 472 removed outlier: 3.731A pdb=" N ALA E 470 " --> pdb=" O ARG E 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER E 552 " --> pdb=" O ALA E 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU E 555 " --> pdb=" O VAL E 551 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 591 Processing helix chain 'E' and resid 593 through 595 No H-bonds generated for 'chain 'E' and resid 593 through 595' Processing helix chain 'E' and resid 603 through 606 No H-bonds generated for 'chain 'E' and resid 603 through 606' Processing helix chain 'E' and resid 623 through 633 removed outlier: 3.634A pdb=" N ALA E 632 " --> pdb=" O ASP E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS E 644 " --> pdb=" O ALA E 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR E 647 " --> pdb=" O MET E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 665 No H-bonds generated for 'chain 'E' and resid 662 through 665' Processing helix chain 'E' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU E 714 " --> pdb=" O ASP E 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG E 717 " --> pdb=" O GLU E 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 718 " --> pdb=" O PHE E 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 719 " --> pdb=" O ALA E 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 721 " --> pdb=" O THR E 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA E 722 " --> pdb=" O PHE E 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 52 No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 76 through 86 Processing helix chain 'F' and resid 129 through 146 Processing helix chain 'F' and resid 150 through 156 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA F 217 " --> pdb=" O GLY F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 Processing helix chain 'F' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 441 Processing helix chain 'F' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY F 451 " --> pdb=" O GLY F 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 452 " --> pdb=" O PRO F 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER F 453 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 455 " --> pdb=" O ARG F 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN F 456 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F 459 " --> pdb=" O GLN F 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 461 " --> pdb=" O THR F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA F 470 " --> pdb=" O ARG F 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL F 472 " --> pdb=" O ALA F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER F 552 " --> pdb=" O ALA F 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU F 555 " --> pdb=" O VAL F 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 557 " --> pdb=" O ARG F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 591 Processing helix chain 'F' and resid 593 through 595 No H-bonds generated for 'chain 'F' and resid 593 through 595' Processing helix chain 'F' and resid 603 through 606 No H-bonds generated for 'chain 'F' and resid 603 through 606' Processing helix chain 'F' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA F 632 " --> pdb=" O ASP F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR F 647 " --> pdb=" O MET F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 665 No H-bonds generated for 'chain 'F' and resid 662 through 665' Processing helix chain 'F' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU F 714 " --> pdb=" O ASP F 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG F 717 " --> pdb=" O GLU F 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 718 " --> pdb=" O PHE F 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE F 719 " --> pdb=" O ALA F 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG F 721 " --> pdb=" O THR F 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 722 " --> pdb=" O PHE F 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 52 No H-bonds generated for 'chain 'G' and resid 49 through 52' Processing helix chain 'G' and resid 76 through 86 Processing helix chain 'G' and resid 129 through 146 Processing helix chain 'G' and resid 150 through 156 Processing helix chain 'G' and resid 176 through 178 No H-bonds generated for 'chain 'G' and resid 176 through 178' Processing helix chain 'G' and resid 181 through 190 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA G 217 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL G 246 " --> pdb=" O ALA G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 274 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA G 309 " --> pdb=" O ALA G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 345 removed outlier: 3.629A pdb=" N THR G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET G 425 " --> pdb=" O GLU G 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 441 Processing helix chain 'G' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY G 451 " --> pdb=" O GLY G 448 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER G 453 " --> pdb=" O ALA G 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE G 455 " --> pdb=" O ARG G 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN G 456 " --> pdb=" O SER G 453 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 459 " --> pdb=" O GLN G 456 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 461 " --> pdb=" O THR G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA G 470 " --> pdb=" O ARG G 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL G 472 " --> pdb=" O ALA G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 558 removed outlier: 3.696A pdb=" N SER G 552 " --> pdb=" O ALA G 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 555 " --> pdb=" O VAL G 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU G 557 " --> pdb=" O ARG G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 591 Processing helix chain 'G' and resid 593 through 595 No H-bonds generated for 'chain 'G' and resid 593 through 595' Processing helix chain 'G' and resid 603 through 606 No H-bonds generated for 'chain 'G' and resid 603 through 606' Processing helix chain 'G' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA G 632 " --> pdb=" O ASP G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS G 644 " --> pdb=" O ALA G 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 647 " --> pdb=" O MET G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 665 No H-bonds generated for 'chain 'G' and resid 662 through 665' Processing helix chain 'G' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU G 714 " --> pdb=" O ASP G 711 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 717 " --> pdb=" O GLU G 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR G 718 " --> pdb=" O PHE G 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE G 719 " --> pdb=" O ALA G 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 721 " --> pdb=" O THR G 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 722 " --> pdb=" O PHE G 719 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 52 No H-bonds generated for 'chain 'H' and resid 49 through 52' Processing helix chain 'H' and resid 76 through 86 Processing helix chain 'H' and resid 129 through 146 Processing helix chain 'H' and resid 150 through 156 Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 181 through 190 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA H 217 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 227 Processing helix chain 'H' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 274 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA H 309 " --> pdb=" O ALA H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR H 344 " --> pdb=" O LEU H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 364 No H-bonds generated for 'chain 'H' and resid 362 through 364' Processing helix chain 'H' and resid 420 through 426 removed outlier: 5.401A pdb=" N MET H 425 " --> pdb=" O GLU H 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 441 Processing helix chain 'H' and resid 448 through 462 removed outlier: 4.032A pdb=" N GLY H 451 " --> pdb=" O GLY H 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG H 452 " --> pdb=" O PRO H 449 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER H 453 " --> pdb=" O ALA H 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE H 455 " --> pdb=" O ARG H 452 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN H 456 " --> pdb=" O SER H 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE H 459 " --> pdb=" O GLN H 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 461 " --> pdb=" O THR H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA H 470 " --> pdb=" O ARG H 466 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL H 472 " --> pdb=" O ALA H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER H 552 " --> pdb=" O ALA H 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU H 555 " --> pdb=" O VAL H 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU H 557 " --> pdb=" O ARG H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 583 through 591 Processing helix chain 'H' and resid 593 through 595 No H-bonds generated for 'chain 'H' and resid 593 through 595' Processing helix chain 'H' and resid 603 through 606 No H-bonds generated for 'chain 'H' and resid 603 through 606' Processing helix chain 'H' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA H 632 " --> pdb=" O ASP H 628 " (cutoff:3.500A) Processing helix chain 'H' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS H 644 " --> pdb=" O ALA H 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR H 647 " --> pdb=" O MET H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 665 No H-bonds generated for 'chain 'H' and resid 662 through 665' Processing helix chain 'H' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU H 714 " --> pdb=" O ASP H 711 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG H 717 " --> pdb=" O GLU H 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 718 " --> pdb=" O PHE H 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE H 719 " --> pdb=" O ALA H 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG H 721 " --> pdb=" O THR H 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 722 " --> pdb=" O PHE H 719 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 52 No H-bonds generated for 'chain 'I' and resid 49 through 52' Processing helix chain 'I' and resid 76 through 86 Processing helix chain 'I' and resid 129 through 146 Processing helix chain 'I' and resid 150 through 156 Processing helix chain 'I' and resid 176 through 178 No H-bonds generated for 'chain 'I' and resid 176 through 178' Processing helix chain 'I' and resid 181 through 190 Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA I 217 " --> pdb=" O GLY I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 239 through 248 removed outlier: 4.385A pdb=" N LYS I 244 " --> pdb=" O SER I 240 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL I 246 " --> pdb=" O ALA I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA I 309 " --> pdb=" O ALA I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR I 344 " --> pdb=" O LEU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 364 No H-bonds generated for 'chain 'I' and resid 362 through 364' Processing helix chain 'I' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 441 Processing helix chain 'I' and resid 448 through 462 removed outlier: 4.032A pdb=" N GLY I 451 " --> pdb=" O GLY I 448 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER I 453 " --> pdb=" O ALA I 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE I 455 " --> pdb=" O ARG I 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN I 456 " --> pdb=" O SER I 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE I 459 " --> pdb=" O GLN I 456 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU I 461 " --> pdb=" O THR I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA I 470 " --> pdb=" O ARG I 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL I 472 " --> pdb=" O ALA I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER I 552 " --> pdb=" O ALA I 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU I 555 " --> pdb=" O VAL I 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU I 557 " --> pdb=" O ARG I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 591 Processing helix chain 'I' and resid 593 through 595 No H-bonds generated for 'chain 'I' and resid 593 through 595' Processing helix chain 'I' and resid 603 through 606 No H-bonds generated for 'chain 'I' and resid 603 through 606' Processing helix chain 'I' and resid 623 through 633 removed outlier: 3.634A pdb=" N ALA I 632 " --> pdb=" O ASP I 628 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 648 removed outlier: 3.805A pdb=" N LYS I 644 " --> pdb=" O ALA I 640 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR I 647 " --> pdb=" O MET I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 665 No H-bonds generated for 'chain 'I' and resid 662 through 665' Processing helix chain 'I' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU I 714 " --> pdb=" O ASP I 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG I 717 " --> pdb=" O GLU I 714 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR I 718 " --> pdb=" O PHE I 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE I 719 " --> pdb=" O ALA I 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG I 721 " --> pdb=" O THR I 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA I 722 " --> pdb=" O PHE I 719 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 36 removed outlier: 3.920A pdb=" N LEU J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 52 No H-bonds generated for 'chain 'J' and resid 49 through 52' Processing helix chain 'J' and resid 76 through 86 Processing helix chain 'J' and resid 129 through 146 Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 190 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 214 through 219 removed outlier: 3.630A pdb=" N ALA J 217 " --> pdb=" O GLY J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 227 Processing helix chain 'J' and resid 239 through 248 removed outlier: 4.386A pdb=" N LYS J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL J 246 " --> pdb=" O ALA J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 274 Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 303 through 309 removed outlier: 3.728A pdb=" N ALA J 309 " --> pdb=" O ALA J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 345 removed outlier: 3.630A pdb=" N THR J 344 " --> pdb=" O LEU J 340 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 364 No H-bonds generated for 'chain 'J' and resid 362 through 364' Processing helix chain 'J' and resid 420 through 426 removed outlier: 5.400A pdb=" N MET J 425 " --> pdb=" O GLU J 421 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 441 Processing helix chain 'J' and resid 448 through 462 removed outlier: 4.033A pdb=" N GLY J 451 " --> pdb=" O GLY J 448 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG J 452 " --> pdb=" O PRO J 449 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER J 453 " --> pdb=" O ALA J 450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE J 455 " --> pdb=" O ARG J 452 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN J 456 " --> pdb=" O SER J 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE J 459 " --> pdb=" O GLN J 456 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU J 461 " --> pdb=" O THR J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 466 through 472 removed outlier: 3.732A pdb=" N ALA J 470 " --> pdb=" O ARG J 466 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL J 472 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 558 removed outlier: 3.695A pdb=" N SER J 552 " --> pdb=" O ALA J 548 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU J 555 " --> pdb=" O VAL J 551 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU J 557 " --> pdb=" O ARG J 553 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 591 Processing helix chain 'J' and resid 593 through 595 No H-bonds generated for 'chain 'J' and resid 593 through 595' Processing helix chain 'J' and resid 603 through 606 No H-bonds generated for 'chain 'J' and resid 603 through 606' Processing helix chain 'J' and resid 623 through 633 removed outlier: 3.633A pdb=" N ALA J 632 " --> pdb=" O ASP J 628 " (cutoff:3.500A) Processing helix chain 'J' and resid 639 through 648 removed outlier: 3.804A pdb=" N LYS J 644 " --> pdb=" O ALA J 640 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR J 647 " --> pdb=" O MET J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 662 through 665 No H-bonds generated for 'chain 'J' and resid 662 through 665' Processing helix chain 'J' and resid 709 through 722 removed outlier: 4.781A pdb=" N GLU J 714 " --> pdb=" O ASP J 711 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG J 717 " --> pdb=" O GLU J 714 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 718 " --> pdb=" O PHE J 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE J 719 " --> pdb=" O ALA J 716 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG J 721 " --> pdb=" O THR J 718 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA J 722 " --> pdb=" O PHE J 719 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU A 10 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 62 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 12 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL A 64 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 64 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 96 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 99 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU A 352 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 388 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE A 354 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA A 324 " --> pdb=" O HIS A 353 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE A 277 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 259 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A 279 " --> pdb=" O VAL A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU A 530 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU A 670 " --> pdb=" O CYS A 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 748 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU B 10 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 62 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 12 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 64 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL B 64 " --> pdb=" O PRO B 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 96 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 99 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU B 352 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 388 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE B 354 " --> pdb=" O THR B 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA B 324 " --> pdb=" O HIS B 353 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 259 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU B 279 " --> pdb=" O VAL B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU B 530 " --> pdb=" O PHE B 570 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU B 670 " --> pdb=" O CYS B 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS B 748 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU C 10 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 62 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL C 12 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL C 64 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL C 64 " --> pdb=" O PRO C 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE C 96 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 99 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 235 removed outlier: 6.291A pdb=" N LEU C 352 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C 388 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE C 354 " --> pdb=" O THR C 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA C 324 " --> pdb=" O HIS C 353 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE C 277 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL C 259 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU C 279 " --> pdb=" O VAL C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU C 530 " --> pdb=" O PHE C 570 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU C 670 " --> pdb=" O CYS C 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 748 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU D 10 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE D 62 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 12 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL D 64 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D 64 " --> pdb=" O PRO D 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE D 96 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 99 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU D 352 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR D 388 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE D 354 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA D 324 " --> pdb=" O HIS D 353 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE D 277 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL D 259 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU D 279 " --> pdb=" O VAL D 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU D 530 " --> pdb=" O PHE D 570 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU D 670 " --> pdb=" O CYS D 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D 748 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU E 10 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE E 62 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL E 12 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL E 64 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL E 64 " --> pdb=" O PRO E 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE E 96 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 99 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU E 352 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR E 388 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE E 354 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA E 324 " --> pdb=" O HIS E 353 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE E 277 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E 259 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU E 279 " --> pdb=" O VAL E 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU E 530 " --> pdb=" O PHE E 570 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU E 670 " --> pdb=" O CYS E 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS E 748 " --> pdb=" O GLU E 670 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU F 10 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE F 62 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 12 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL F 64 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL F 64 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE F 96 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY F 99 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU F 352 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR F 388 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE F 354 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA F 324 " --> pdb=" O HIS F 353 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE F 277 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL F 259 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU F 279 " --> pdb=" O VAL F 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU F 530 " --> pdb=" O PHE F 570 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU F 670 " --> pdb=" O CYS F 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS F 748 " --> pdb=" O GLU F 670 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU G 10 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE G 62 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL G 12 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL G 64 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL G 64 " --> pdb=" O PRO G 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE G 96 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY G 99 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU G 352 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR G 388 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE G 354 " --> pdb=" O THR G 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA G 324 " --> pdb=" O HIS G 353 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE G 277 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL G 259 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU G 279 " --> pdb=" O VAL G 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU G 530 " --> pdb=" O PHE G 570 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 669 through 673 removed outlier: 3.827A pdb=" N GLU G 670 " --> pdb=" O CYS G 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS G 748 " --> pdb=" O GLU G 670 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU H 10 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE H 62 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL H 12 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL H 64 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL H 64 " --> pdb=" O PRO H 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE H 96 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY H 99 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU H 352 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR H 388 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE H 354 " --> pdb=" O THR H 388 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA H 324 " --> pdb=" O HIS H 353 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE H 277 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL H 259 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU H 279 " --> pdb=" O VAL H 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU H 530 " --> pdb=" O PHE H 570 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU H 670 " --> pdb=" O CYS H 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS H 748 " --> pdb=" O GLU H 670 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU I 10 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE I 62 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL I 12 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL I 64 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL I 64 " --> pdb=" O PRO I 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE I 96 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY I 99 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU I 352 " --> pdb=" O PHE I 386 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR I 388 " --> pdb=" O LEU I 352 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE I 354 " --> pdb=" O THR I 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA I 324 " --> pdb=" O HIS I 353 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE I 277 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL I 259 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU I 279 " --> pdb=" O VAL I 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'I' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU I 530 " --> pdb=" O PHE I 570 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU I 670 " --> pdb=" O CYS I 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS I 748 " --> pdb=" O GLU I 670 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 41 through 43 removed outlier: 7.289A pdb=" N LEU J 10 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE J 62 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL J 12 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL J 64 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL J 64 " --> pdb=" O PRO J 94 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE J 96 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY J 99 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'J' and resid 231 through 235 removed outlier: 6.292A pdb=" N LEU J 352 " --> pdb=" O PHE J 386 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR J 388 " --> pdb=" O LEU J 352 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE J 354 " --> pdb=" O THR J 388 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA J 324 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 256 through 260 removed outlier: 6.816A pdb=" N ILE J 277 " --> pdb=" O VAL J 257 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL J 259 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU J 279 " --> pdb=" O VAL J 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'J' and resid 529 through 531 removed outlier: 3.633A pdb=" N LEU J 530 " --> pdb=" O PHE J 570 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 669 through 673 removed outlier: 3.826A pdb=" N GLU J 670 " --> pdb=" O CYS J 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS J 748 " --> pdb=" O GLU J 670 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 2640 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: 17.16 Time building geometry restraints manager: 18.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17190 1.33 - 1.45: 10878 1.45 - 1.57: 30072 1.57 - 1.69: 0 1.69 - 1.81: 410 Bond restraints: 58550 Sorted by residual: bond pdb=" O4P PLP I 801 " pdb=" P PLP I 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" O4P PLP D 801 " pdb=" P PLP D 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" O4P PLP G 801 " pdb=" P PLP G 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" O4P PLP B 801 " pdb=" P PLP B 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" O4P PLP E 801 " pdb=" P PLP E 801 " ideal model delta sigma weight residual 1.610 1.780 -0.170 2.00e-02 2.50e+03 7.22e+01 ... (remaining 58545 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.72: 1214 104.72 - 112.10: 27581 112.10 - 119.48: 21424 119.48 - 126.86: 28431 126.86 - 134.23: 990 Bond angle restraints: 79640 Sorted by residual: angle pdb=" CA HIS G 392 " pdb=" C HIS G 392 " pdb=" N LYS G 393 " ideal model delta sigma weight residual 118.55 104.79 13.76 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS D 392 " pdb=" C HIS D 392 " pdb=" N LYS D 393 " ideal model delta sigma weight residual 118.55 104.80 13.75 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS I 392 " pdb=" C HIS I 392 " pdb=" N LYS I 393 " ideal model delta sigma weight residual 118.55 104.80 13.75 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS E 392 " pdb=" C HIS E 392 " pdb=" N LYS E 393 " ideal model delta sigma weight residual 118.55 104.80 13.75 1.24e+00 6.50e-01 1.23e+02 angle pdb=" CA HIS H 392 " pdb=" C HIS H 392 " pdb=" N LYS H 393 " ideal model delta sigma weight residual 118.55 104.81 13.74 1.24e+00 6.50e-01 1.23e+02 ... (remaining 79635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.69: 31778 23.69 - 47.39: 2522 47.39 - 71.08: 220 71.08 - 94.78: 80 94.78 - 118.47: 10 Dihedral angle restraints: 34610 sinusoidal: 13150 harmonic: 21460 Sorted by residual: dihedral pdb=" CA VAL E 203 " pdb=" C VAL E 203 " pdb=" N PRO E 204 " pdb=" CA PRO E 204 " ideal model delta harmonic sigma weight residual -180.00 -133.23 -46.77 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CA VAL J 203 " pdb=" C VAL J 203 " pdb=" N PRO J 204 " pdb=" CA PRO J 204 " ideal model delta harmonic sigma weight residual -180.00 -133.23 -46.77 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CA VAL A 203 " pdb=" C VAL A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta harmonic sigma weight residual 180.00 -133.24 -46.76 0 5.00e+00 4.00e-02 8.75e+01 ... (remaining 34607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6649 0.066 - 0.131: 1963 0.131 - 0.197: 218 0.197 - 0.263: 40 0.263 - 0.328: 30 Chirality restraints: 8900 Sorted by residual: chirality pdb=" CA THR C 168 " pdb=" N THR C 168 " pdb=" C THR C 168 " pdb=" CB THR C 168 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR E 168 " pdb=" N THR E 168 " pdb=" C THR E 168 " pdb=" CB THR E 168 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR G 168 " pdb=" N THR G 168 " pdb=" C THR G 168 " pdb=" CB THR G 168 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 8897 not shown) Planarity restraints: 10360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS E 392 " -0.034 2.00e-02 2.50e+03 7.52e-02 5.65e+01 pdb=" C HIS E 392 " 0.130 2.00e-02 2.50e+03 pdb=" O HIS E 392 " -0.055 2.00e-02 2.50e+03 pdb=" N LYS E 393 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 392 " 0.034 2.00e-02 2.50e+03 7.51e-02 5.65e+01 pdb=" C HIS C 392 " -0.129 2.00e-02 2.50e+03 pdb=" O HIS C 392 " 0.055 2.00e-02 2.50e+03 pdb=" N LYS C 393 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 392 " 0.034 2.00e-02 2.50e+03 7.51e-02 5.64e+01 pdb=" C HIS D 392 " -0.129 2.00e-02 2.50e+03 pdb=" O HIS D 392 " 0.055 2.00e-02 2.50e+03 pdb=" N LYS D 393 " 0.041 2.00e-02 2.50e+03 ... (remaining 10357 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 13125 2.78 - 3.31: 52702 3.31 - 3.84: 97802 3.84 - 4.37: 114034 4.37 - 4.90: 189597 Nonbonded interactions: 467260 Sorted by model distance: nonbonded pdb=" O SER E 197 " pdb=" OG SER E 197 " model vdw 2.244 2.440 nonbonded pdb=" O SER C 197 " pdb=" OG SER C 197 " model vdw 2.245 2.440 nonbonded pdb=" O SER H 197 " pdb=" OG SER H 197 " model vdw 2.245 2.440 nonbonded pdb=" O SER I 197 " pdb=" OG SER I 197 " model vdw 2.245 2.440 nonbonded pdb=" O SER F 197 " pdb=" OG SER F 197 " model vdw 2.245 2.440 ... (remaining 467255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.060 Check model and map are aligned: 0.620 Set scattering table: 0.420 Process input model: 113.610 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.009 0.170 58550 Z= 0.585 Angle : 1.224 17.933 79640 Z= 0.649 Chirality : 0.063 0.328 8900 Planarity : 0.008 0.075 10360 Dihedral : 17.031 118.474 20850 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 16.71 % Favored : 83.03 % Rotamer: Outliers : 1.89 % Allowed : 15.32 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.56 % 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: -5.81 (0.07), residues: 7470 helix: -4.07 (0.06), residues: 2720 sheet: -4.11 (0.11), residues: 960 loop : -3.61 (0.08), residues: 3790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP B 486 HIS 0.008 0.002 HIS H 187 PHE 0.027 0.003 PHE J 570 TYR 0.062 0.004 TYR C 359 ARG 0.014 0.001 ARG E 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1372 time to evaluate : 4.674 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: A 81 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7669 (mp0) REVERT: A 104 ILE cc_start: 0.8730 (mt) cc_final: 0.8405 (mt) REVERT: A 143 TYR cc_start: 0.8241 (t80) cc_final: 0.7965 (t80) REVERT: A 240 SER cc_start: 0.8835 (m) cc_final: 0.8366 (t) REVERT: A 273 MET cc_start: 0.7284 (mpp) cc_final: 0.7074 (mmp) REVERT: A 440 ASP cc_start: 0.8403 (t0) cc_final: 0.8164 (t0) REVERT: A 521 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8959 (t) REVERT: A 718 THR cc_start: 0.8643 (t) cc_final: 0.8357 (p) REVERT: B 81 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7640 (mp0) REVERT: B 104 ILE cc_start: 0.8763 (mt) cc_final: 0.8377 (mt) REVERT: B 143 TYR cc_start: 0.8274 (t80) cc_final: 0.8012 (t80) REVERT: B 240 SER cc_start: 0.8774 (m) cc_final: 0.8352 (t) REVERT: B 440 ASP cc_start: 0.8439 (t0) cc_final: 0.8049 (t0) REVERT: B 646 MET cc_start: 0.7536 (ptt) cc_final: 0.7210 (ptm) REVERT: B 743 CYS cc_start: 0.7745 (m) cc_final: 0.7519 (m) REVERT: C 81 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7690 (mp0) REVERT: C 104 ILE cc_start: 0.8732 (mt) cc_final: 0.8336 (mt) REVERT: C 143 TYR cc_start: 0.8285 (t80) cc_final: 0.8071 (t80) REVERT: C 240 SER cc_start: 0.8723 (m) cc_final: 0.8385 (t) REVERT: C 519 ASP cc_start: 0.6052 (t0) cc_final: 0.5773 (t0) REVERT: C 558 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7750 (mmt-90) REVERT: C 646 MET cc_start: 0.7618 (ptt) cc_final: 0.7051 (ptm) REVERT: D 27 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7795 (mtm-85) REVERT: D 81 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7677 (mp0) REVERT: D 104 ILE cc_start: 0.8718 (mt) cc_final: 0.8379 (mt) REVERT: D 143 TYR cc_start: 0.8223 (t80) cc_final: 0.7981 (t80) REVERT: D 240 SER cc_start: 0.8821 (m) cc_final: 0.8497 (t) REVERT: D 521 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8925 (t) REVERT: D 718 THR cc_start: 0.8674 (t) cc_final: 0.8453 (p) REVERT: E 81 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7594 (mp0) REVERT: E 104 ILE cc_start: 0.8760 (mt) cc_final: 0.8425 (mt) REVERT: E 143 TYR cc_start: 0.8181 (t80) cc_final: 0.7942 (t80) REVERT: E 389 HIS cc_start: 0.8316 (m-70) cc_final: 0.8057 (m90) REVERT: E 492 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6828 (tm-30) REVERT: E 521 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9003 (t) REVERT: E 558 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.7661 (mmt-90) REVERT: E 718 THR cc_start: 0.8823 (t) cc_final: 0.8615 (p) REVERT: F 81 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7664 (mp0) REVERT: F 104 ILE cc_start: 0.8732 (mt) cc_final: 0.8408 (mt) REVERT: F 143 TYR cc_start: 0.8237 (t80) cc_final: 0.7961 (t80) REVERT: F 240 SER cc_start: 0.8847 (m) cc_final: 0.8386 (t) REVERT: F 440 ASP cc_start: 0.8406 (t0) cc_final: 0.8165 (t0) REVERT: F 521 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8961 (t) REVERT: F 718 THR cc_start: 0.8644 (t) cc_final: 0.8355 (p) REVERT: G 81 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7644 (mp0) REVERT: G 104 ILE cc_start: 0.8761 (mt) cc_final: 0.8375 (mt) REVERT: G 143 TYR cc_start: 0.8278 (t80) cc_final: 0.8013 (t80) REVERT: G 240 SER cc_start: 0.8782 (m) cc_final: 0.8359 (t) REVERT: G 440 ASP cc_start: 0.8437 (t0) cc_final: 0.8064 (t0) REVERT: G 646 MET cc_start: 0.7532 (ptt) cc_final: 0.7212 (ptm) REVERT: G 743 CYS cc_start: 0.7743 (m) cc_final: 0.7518 (m) REVERT: H 81 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7688 (mp0) REVERT: H 104 ILE cc_start: 0.8727 (mt) cc_final: 0.8329 (mt) REVERT: H 143 TYR cc_start: 0.8278 (t80) cc_final: 0.8067 (t80) REVERT: H 240 SER cc_start: 0.8728 (m) cc_final: 0.8386 (t) REVERT: H 519 ASP cc_start: 0.6047 (t0) cc_final: 0.5765 (t0) REVERT: H 558 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.7754 (mmt-90) REVERT: H 646 MET cc_start: 0.7612 (ptt) cc_final: 0.7046 (ptm) REVERT: I 27 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7795 (mtm-85) REVERT: I 81 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7676 (mp0) REVERT: I 104 ILE cc_start: 0.8717 (mt) cc_final: 0.8382 (mt) REVERT: I 143 TYR cc_start: 0.8222 (t80) cc_final: 0.7979 (t80) REVERT: I 240 SER cc_start: 0.8836 (m) cc_final: 0.8513 (t) REVERT: I 521 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8925 (t) REVERT: I 718 THR cc_start: 0.8679 (t) cc_final: 0.8459 (p) REVERT: J 81 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7588 (mp0) REVERT: J 104 ILE cc_start: 0.8760 (mt) cc_final: 0.8427 (mt) REVERT: J 143 TYR cc_start: 0.8180 (t80) cc_final: 0.7939 (t80) REVERT: J 389 HIS cc_start: 0.8308 (m-70) cc_final: 0.8056 (m90) REVERT: J 492 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6829 (tm-30) REVERT: J 521 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9004 (t) REVERT: J 558 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7661 (mmt-90) REVERT: J 718 THR cc_start: 0.8820 (t) cc_final: 0.8614 (p) outliers start: 110 outliers final: 48 residues processed: 1452 average time/residue: 0.5954 time to fit residues: 1427.9957 Evaluate side-chains 1103 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1049 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 584 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 584 SER Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 393 LYS Chi-restraints excluded: chain H residue 584 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 393 LYS Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 584 SER Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 393 LYS Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 584 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.9990 chunk 568 optimal weight: 0.8980 chunk 315 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 383 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 587 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 357 optimal weight: 0.5980 chunk 437 optimal weight: 2.9990 chunk 681 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 171 HIS A 243 ASN A 343 GLN A 365 HIS ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 420 ASN A 456 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 171 HIS B 187 HIS B 243 ASN B 343 GLN B 365 HIS B 400 GLN B 456 GLN C 92 GLN C 171 HIS C 187 HIS C 243 ASN C 343 GLN C 365 HIS ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 171 HIS D 187 HIS D 243 ASN D 343 GLN D 365 HIS ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 GLN D 420 ASN D 456 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN E 92 GLN E 171 HIS E 243 ASN E 343 GLN E 365 HIS E 400 GLN E 420 ASN E 456 GLN F 92 GLN F 171 HIS F 243 ASN F 343 GLN F 365 HIS ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN F 420 ASN F 456 GLN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 171 HIS G 187 HIS G 243 ASN G 343 GLN G 365 HIS G 400 GLN G 456 GLN H 92 GLN H 171 HIS H 187 HIS H 243 ASN H 343 GLN H 365 HIS ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 GLN ** H 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 456 GLN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN I 171 HIS I 187 HIS I 243 ASN I 343 GLN I 365 HIS ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 400 GLN I 420 ASN I 456 GLN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN J 171 HIS J 243 ASN J 343 GLN J 365 HIS J 400 GLN J 420 ASN J 456 GLN ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 58550 Z= 0.189 Angle : 0.716 13.717 79640 Z= 0.360 Chirality : 0.045 0.216 8900 Planarity : 0.005 0.074 10360 Dihedral : 8.307 68.517 8244 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 4.22 % Allowed : 20.15 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -4.84 (0.08), residues: 7470 helix: -3.19 (0.07), residues: 2690 sheet: -3.44 (0.13), residues: 860 loop : -3.20 (0.09), residues: 3920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 486 HIS 0.004 0.001 HIS C 392 PHE 0.014 0.001 PHE E 593 TYR 0.029 0.002 TYR J 359 ARG 0.007 0.000 ARG J 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1192 time to evaluate : 4.749 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: 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 48 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 81 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7615 (mp0) REVERT: A 240 SER cc_start: 0.8712 (m) cc_final: 0.8287 (t) REVERT: A 273 MET cc_start: 0.7107 (mpp) cc_final: 0.6880 (mpp) REVERT: A 398 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8910 (m-80) REVERT: A 420 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7568 (m-40) REVERT: A 521 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8883 (t) REVERT: A 718 THR cc_start: 0.8509 (t) cc_final: 0.8185 (p) REVERT: B 81 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7667 (mp0) REVERT: B 184 GLN cc_start: 0.7620 (tt0) cc_final: 0.7408 (tt0) REVERT: B 240 SER cc_start: 0.8823 (m) cc_final: 0.8382 (t) REVERT: B 398 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8960 (m-10) REVERT: B 440 ASP cc_start: 0.8137 (t0) cc_final: 0.7927 (t0) REVERT: B 521 VAL cc_start: 0.9056 (t) cc_final: 0.8741 (t) REVERT: B 689 TYR cc_start: 0.6587 (t80) cc_final: 0.6126 (m-10) REVERT: C 81 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7642 (mp0) REVERT: C 240 SER cc_start: 0.8775 (m) cc_final: 0.8393 (t) REVERT: C 273 MET cc_start: 0.7227 (mpp) cc_final: 0.7004 (mmp) REVERT: C 445 MET cc_start: 0.7551 (mtp) cc_final: 0.7342 (ttm) REVERT: C 492 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6783 (tm-30) REVERT: C 689 TYR cc_start: 0.6607 (t80) cc_final: 0.6096 (m-10) REVERT: C 697 MET cc_start: 0.6268 (ptt) cc_final: 0.6052 (ptt) REVERT: D 81 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7652 (mp0) REVERT: D 240 SER cc_start: 0.8885 (m) cc_final: 0.8447 (t) REVERT: D 420 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7410 (m-40) REVERT: D 521 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8815 (t) REVERT: D 689 TYR cc_start: 0.6529 (t80) cc_final: 0.6072 (m-10) REVERT: D 718 THR cc_start: 0.8606 (t) cc_final: 0.8375 (p) REVERT: E 48 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7903 (mt-10) REVERT: E 81 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7588 (mp0) REVERT: E 104 ILE cc_start: 0.8704 (mt) cc_final: 0.8484 (mt) REVERT: E 166 TRP cc_start: 0.8225 (t-100) cc_final: 0.7779 (t-100) REVERT: E 247 TRP cc_start: 0.7787 (m100) cc_final: 0.7481 (m100) REVERT: E 394 MET cc_start: 0.7979 (mmm) cc_final: 0.7747 (mmm) REVERT: E 492 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6645 (tm-30) REVERT: E 521 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8915 (t) REVERT: E 689 TYR cc_start: 0.6458 (t80) cc_final: 0.6002 (m-10) REVERT: E 718 THR cc_start: 0.8692 (t) cc_final: 0.8479 (p) REVERT: F 48 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7837 (mt-10) REVERT: F 81 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7613 (mp0) REVERT: F 240 SER cc_start: 0.8725 (m) cc_final: 0.8310 (t) REVERT: F 398 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8906 (m-80) REVERT: F 420 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7569 (m-40) REVERT: F 521 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8883 (t) REVERT: F 718 THR cc_start: 0.8512 (t) cc_final: 0.8188 (p) REVERT: G 81 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7666 (mp0) REVERT: G 184 GLN cc_start: 0.7621 (tt0) cc_final: 0.7409 (tt0) REVERT: G 240 SER cc_start: 0.8829 (m) cc_final: 0.8386 (t) REVERT: G 398 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8958 (m-10) REVERT: G 440 ASP cc_start: 0.8135 (t0) cc_final: 0.7922 (t0) REVERT: G 521 VAL cc_start: 0.9058 (t) cc_final: 0.8733 (t) REVERT: G 689 TYR cc_start: 0.6580 (t80) cc_final: 0.6127 (m-10) REVERT: H 81 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7640 (mp0) REVERT: H 240 SER cc_start: 0.8780 (m) cc_final: 0.8392 (t) REVERT: H 273 MET cc_start: 0.7273 (mpp) cc_final: 0.7018 (mmp) REVERT: H 440 ASP cc_start: 0.8200 (t0) cc_final: 0.7998 (t0) REVERT: H 445 MET cc_start: 0.7528 (mtp) cc_final: 0.7309 (ttm) REVERT: H 492 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6781 (tm-30) REVERT: H 689 TYR cc_start: 0.6614 (t80) cc_final: 0.6099 (m-10) REVERT: H 697 MET cc_start: 0.6274 (ptt) cc_final: 0.6066 (ptt) REVERT: I 81 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7652 (mp0) REVERT: I 240 SER cc_start: 0.8900 (m) cc_final: 0.8462 (t) REVERT: I 420 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7400 (m-40) REVERT: I 521 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8816 (t) REVERT: I 689 TYR cc_start: 0.6524 (t80) cc_final: 0.6061 (m-10) REVERT: I 718 THR cc_start: 0.8609 (t) cc_final: 0.8381 (p) REVERT: J 48 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7903 (mt-10) REVERT: J 81 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7578 (mp0) REVERT: J 104 ILE cc_start: 0.8702 (mt) cc_final: 0.8485 (mt) REVERT: J 166 TRP cc_start: 0.8226 (t-100) cc_final: 0.7782 (t-100) REVERT: J 247 TRP cc_start: 0.7771 (m100) cc_final: 0.7475 (m100) REVERT: J 394 MET cc_start: 0.7977 (mmm) cc_final: 0.7745 (mmm) REVERT: J 492 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6652 (tm-30) REVERT: J 521 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8915 (t) REVERT: J 689 TYR cc_start: 0.6460 (t80) cc_final: 0.6011 (m-10) REVERT: J 718 THR cc_start: 0.8693 (t) cc_final: 0.8480 (p) outliers start: 245 outliers final: 162 residues processed: 1325 average time/residue: 0.6083 time to fit residues: 1344.4789 Evaluate side-chains 1199 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1023 time to evaluate : 4.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 398 PHE Chi-restraints excluded: chain D residue 420 ASN Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 393 LYS Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 420 ASN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 658 SER Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 393 LYS Chi-restraints excluded: chain H residue 398 PHE Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 555 LEU Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 393 LYS Chi-restraints excluded: chain I residue 398 PHE Chi-restraints excluded: chain I residue 420 ASN Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 371 ARG Chi-restraints excluded: chain J residue 393 LYS Chi-restraints excluded: chain J residue 420 ASN Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 9.9990 chunk 211 optimal weight: 50.0000 chunk 566 optimal weight: 7.9990 chunk 463 optimal weight: 1.9990 chunk 187 optimal weight: 0.3980 chunk 682 optimal weight: 9.9990 chunk 737 optimal weight: 7.9990 chunk 607 optimal weight: 10.0000 chunk 676 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 547 optimal weight: 8.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 187 HIS ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 471 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 226 ASN B 262 ASN ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** E 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN F 187 HIS ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 ASN ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 226 ASN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 471 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 471 ASN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 GLN J 187 HIS ** J 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 471 ASN ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 58550 Z= 0.498 Angle : 0.869 11.834 79640 Z= 0.442 Chirality : 0.051 0.225 8900 Planarity : 0.006 0.083 10360 Dihedral : 8.244 55.182 8220 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.90 % Favored : 81.97 % Rotamer: Outliers : 6.57 % Allowed : 22.55 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.03 % 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: -4.63 (0.08), residues: 7470 helix: -2.82 (0.08), residues: 2750 sheet: -3.72 (0.13), residues: 850 loop : -3.13 (0.09), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 247 HIS 0.006 0.001 HIS I 212 PHE 0.021 0.003 PHE H 723 TYR 0.032 0.003 TYR G 433 ARG 0.005 0.001 ARG H 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1063 time to evaluate : 4.805 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 81 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7535 (mp0) REVERT: A 104 ILE cc_start: 0.8756 (mt) cc_final: 0.8431 (mt) REVERT: A 240 SER cc_start: 0.8826 (m) cc_final: 0.8492 (t) REVERT: A 371 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6643 (tpp-160) REVERT: A 398 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: A 424 MET cc_start: 0.8084 (mmm) cc_final: 0.7842 (mmt) REVERT: A 471 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7753 (t0) REVERT: A 555 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7132 (pp) REVERT: B 240 SER cc_start: 0.8852 (m) cc_final: 0.8560 (t) REVERT: B 398 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8999 (m-10) REVERT: B 440 ASP cc_start: 0.8435 (t0) cc_final: 0.8212 (t0) REVERT: B 592 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: B 689 TYR cc_start: 0.6628 (t80) cc_final: 0.6255 (m-10) REVERT: C 81 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7668 (mp0) REVERT: C 240 SER cc_start: 0.8931 (m) cc_final: 0.8625 (t) REVERT: C 555 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7249 (pp) REVERT: D 240 SER cc_start: 0.8959 (m) cc_final: 0.8607 (t) REVERT: D 521 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8841 (t) REVERT: E 81 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7585 (mp0) REVERT: E 104 ILE cc_start: 0.8850 (mt) cc_final: 0.8545 (mt) REVERT: E 187 HIS cc_start: 0.8676 (t70) cc_final: 0.8475 (t70) REVERT: E 192 GLU cc_start: 0.6600 (mp0) cc_final: 0.6376 (mp0) REVERT: E 371 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6495 (tpp-160) REVERT: E 492 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6525 (tm-30) REVERT: E 521 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9178 (t) REVERT: E 555 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7264 (pp) REVERT: F 81 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7529 (mp0) REVERT: F 104 ILE cc_start: 0.8760 (mt) cc_final: 0.8434 (mt) REVERT: F 240 SER cc_start: 0.8831 (m) cc_final: 0.8507 (t) REVERT: F 371 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6643 (tpp-160) REVERT: F 398 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: F 424 MET cc_start: 0.8081 (mmm) cc_final: 0.7818 (mmt) REVERT: F 471 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7751 (t0) REVERT: F 555 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7124 (pp) REVERT: G 240 SER cc_start: 0.8859 (m) cc_final: 0.8564 (t) REVERT: G 398 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8998 (m-10) REVERT: G 440 ASP cc_start: 0.8437 (t0) cc_final: 0.8211 (t0) REVERT: G 592 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: G 689 TYR cc_start: 0.6617 (t80) cc_final: 0.6254 (m-10) REVERT: H 81 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7668 (mp0) REVERT: H 240 SER cc_start: 0.8935 (m) cc_final: 0.8632 (t) REVERT: H 440 ASP cc_start: 0.8420 (t0) cc_final: 0.8180 (t0) REVERT: H 555 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7254 (pp) REVERT: I 240 SER cc_start: 0.8981 (m) cc_final: 0.8634 (t) REVERT: I 389 HIS cc_start: 0.8389 (m90) cc_final: 0.8146 (m90) REVERT: I 440 ASP cc_start: 0.8522 (t70) cc_final: 0.8314 (t0) REVERT: I 521 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8844 (t) REVERT: J 81 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7604 (mp0) REVERT: J 104 ILE cc_start: 0.8852 (mt) cc_final: 0.8552 (mt) REVERT: J 187 HIS cc_start: 0.8679 (t70) cc_final: 0.8474 (t70) REVERT: J 192 GLU cc_start: 0.6602 (mp0) cc_final: 0.6374 (mp0) REVERT: J 371 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6499 (tpp-160) REVERT: J 492 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6525 (tm-30) REVERT: J 521 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9179 (t) REVERT: J 555 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7259 (pp) outliers start: 382 outliers final: 272 residues processed: 1311 average time/residue: 0.5263 time to fit residues: 1180.7280 Evaluate side-chains 1293 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 999 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 486 TRP Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 718 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 398 PHE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 361 TYR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 371 ARG Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 167 HIS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 359 TYR Chi-restraints excluded: chain F residue 361 TYR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 371 ARG Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 420 ASN Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain F residue 471 ASN Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain F residue 729 ASP Chi-restraints excluded: chain F residue 746 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 486 TRP Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 569 SER Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 592 GLU Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain G residue 746 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 361 TYR Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 388 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 555 LEU Chi-restraints excluded: chain H residue 569 SER Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 664 LEU Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain H residue 718 THR Chi-restraints excluded: chain H residue 746 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 361 TYR Chi-restraints excluded: chain I residue 398 PHE Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 729 ASP Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain I residue 746 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 197 SER Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 361 TYR Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 371 ARG Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 526 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 565 THR Chi-restraints excluded: chain J residue 569 SER Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 696 ILE Chi-restraints excluded: chain J residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 0.0470 chunk 512 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 458 optimal weight: 6.9990 chunk 684 optimal weight: 0.6980 chunk 724 optimal weight: 0.0980 chunk 357 optimal weight: 1.9990 chunk 648 optimal weight: 0.4980 chunk 195 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 471 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN ** G 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN H 471 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58550 Z= 0.181 Angle : 0.700 12.455 79640 Z= 0.348 Chirality : 0.045 0.199 8900 Planarity : 0.005 0.075 10360 Dihedral : 7.227 52.196 8168 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 4.97 % Allowed : 25.44 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -4.26 (0.09), residues: 7470 helix: -2.43 (0.09), residues: 2750 sheet: -3.38 (0.13), residues: 860 loop : -3.02 (0.09), residues: 3860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 247 HIS 0.005 0.001 HIS H 392 PHE 0.014 0.001 PHE I 570 TYR 0.025 0.002 TYR G 359 ARG 0.009 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1062 time to evaluate : 4.778 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: A 75 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6506 (tt) REVERT: A 81 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7593 (mp0) REVERT: A 227 PHE cc_start: 0.8333 (m-80) cc_final: 0.8097 (m-10) REVERT: A 240 SER cc_start: 0.8830 (m) cc_final: 0.8406 (t) REVERT: A 398 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: B 240 SER cc_start: 0.8850 (m) cc_final: 0.8469 (t) REVERT: B 398 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8920 (m-10) REVERT: B 440 ASP cc_start: 0.8247 (t0) cc_final: 0.8038 (t0) REVERT: B 558 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.7146 (mtt90) REVERT: C 240 SER cc_start: 0.8777 (m) cc_final: 0.8410 (t) REVERT: C 273 MET cc_start: 0.6730 (mmp) cc_final: 0.6395 (mmt) REVERT: C 334 LEU cc_start: 0.8823 (mm) cc_final: 0.8475 (mm) REVERT: C 492 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 519 ASP cc_start: 0.6526 (t0) cc_final: 0.6127 (t70) REVERT: D 75 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6573 (tt) REVERT: D 81 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7607 (mp0) REVERT: D 240 SER cc_start: 0.8910 (m) cc_final: 0.8495 (t) REVERT: D 424 MET cc_start: 0.7896 (mmm) cc_final: 0.7662 (mmt) REVERT: E 48 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7651 (mt-10) REVERT: E 75 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6368 (tt) REVERT: E 81 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7537 (mp0) REVERT: E 104 ILE cc_start: 0.8840 (mt) cc_final: 0.8578 (mt) REVERT: E 166 TRP cc_start: 0.8157 (t-100) cc_final: 0.7692 (t-100) REVERT: E 227 PHE cc_start: 0.8374 (m-80) cc_final: 0.8016 (m-80) REVERT: E 492 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6531 (tm-30) REVERT: E 521 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8765 (p) REVERT: F 75 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6504 (tt) REVERT: F 81 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7591 (mp0) REVERT: F 227 PHE cc_start: 0.8331 (m-80) cc_final: 0.8094 (m-10) REVERT: F 240 SER cc_start: 0.8836 (m) cc_final: 0.8414 (t) REVERT: F 398 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8853 (m-80) REVERT: G 240 SER cc_start: 0.8860 (m) cc_final: 0.8478 (t) REVERT: G 398 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (m-10) REVERT: G 440 ASP cc_start: 0.8244 (t0) cc_final: 0.8034 (t0) REVERT: G 558 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7153 (mtt90) REVERT: H 240 SER cc_start: 0.8777 (m) cc_final: 0.8417 (t) REVERT: H 334 LEU cc_start: 0.8818 (mm) cc_final: 0.8468 (mm) REVERT: H 440 ASP cc_start: 0.8297 (t0) cc_final: 0.8075 (t0) REVERT: H 492 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6715 (tm-30) REVERT: H 519 ASP cc_start: 0.6516 (t0) cc_final: 0.6020 (t70) REVERT: I 75 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6571 (tt) REVERT: I 81 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7603 (mp0) REVERT: I 240 SER cc_start: 0.8924 (m) cc_final: 0.8500 (t) REVERT: I 424 MET cc_start: 0.7905 (mmm) cc_final: 0.7669 (mmt) REVERT: J 48 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7657 (mt-10) REVERT: J 75 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6397 (tt) REVERT: J 81 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7535 (mp0) REVERT: J 104 ILE cc_start: 0.8842 (mt) cc_final: 0.8581 (mt) REVERT: J 166 TRP cc_start: 0.8160 (t-100) cc_final: 0.7697 (t-100) REVERT: J 227 PHE cc_start: 0.8368 (m-80) cc_final: 0.8016 (m-80) REVERT: J 492 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6532 (tm-30) REVERT: J 521 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8769 (p) outliers start: 289 outliers final: 203 residues processed: 1229 average time/residue: 0.5380 time to fit residues: 1120.7776 Evaluate side-chains 1186 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 971 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 398 PHE Chi-restraints excluded: chain D residue 420 ASN Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 359 TYR Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 420 ASN Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 526 ILE Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 664 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 398 PHE Chi-restraints excluded: chain I residue 420 ASN Chi-restraints excluded: chain I residue 421 GLU Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 526 ILE Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 4.9990 chunk 411 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 539 optimal weight: 7.9990 chunk 299 optimal weight: 0.0370 chunk 618 optimal weight: 0.6980 chunk 501 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 chunk 650 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58550 Z= 0.188 Angle : 0.683 11.767 79640 Z= 0.336 Chirality : 0.044 0.207 8900 Planarity : 0.005 0.074 10360 Dihedral : 6.938 51.420 8164 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % Rotamer: Outliers : 4.78 % Allowed : 26.73 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -4.05 (0.09), residues: 7470 helix: -2.27 (0.09), residues: 2740 sheet: -3.13 (0.14), residues: 840 loop : -2.92 (0.09), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 247 HIS 0.004 0.001 HIS G 231 PHE 0.018 0.001 PHE I 367 TYR 0.024 0.002 TYR E 359 ARG 0.014 0.000 ARG J 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1025 time to evaluate : 4.783 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: A 81 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7614 (mp0) REVERT: A 166 TRP cc_start: 0.8137 (t-100) cc_final: 0.7834 (t-100) REVERT: A 227 PHE cc_start: 0.8304 (m-80) cc_final: 0.8042 (m-10) REVERT: A 240 SER cc_start: 0.8781 (m) cc_final: 0.8388 (t) REVERT: A 398 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8879 (m-80) REVERT: B 240 SER cc_start: 0.8840 (m) cc_final: 0.8457 (t) REVERT: B 334 LEU cc_start: 0.8835 (mm) cc_final: 0.7754 (tp) REVERT: B 398 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8913 (m-10) REVERT: C 240 SER cc_start: 0.8788 (m) cc_final: 0.8438 (t) REVERT: C 273 MET cc_start: 0.6699 (mmp) cc_final: 0.6389 (mmp) REVERT: C 334 LEU cc_start: 0.8819 (mm) cc_final: 0.8406 (mm) REVERT: C 420 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7465 (t0) REVERT: C 492 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6742 (tm-30) REVERT: C 646 MET cc_start: 0.6658 (ptt) cc_final: 0.6318 (ptt) REVERT: C 685 MET cc_start: 0.6938 (tpt) cc_final: 0.6663 (tpt) REVERT: D 240 SER cc_start: 0.8891 (m) cc_final: 0.8480 (t) REVERT: D 424 MET cc_start: 0.7867 (mmm) cc_final: 0.7649 (mmt) REVERT: D 492 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6781 (tm-30) REVERT: E 81 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7564 (mp0) REVERT: E 104 ILE cc_start: 0.8817 (mt) cc_final: 0.8547 (mt) REVERT: E 166 TRP cc_start: 0.8158 (t-100) cc_final: 0.7757 (t-100) REVERT: E 371 ARG cc_start: 0.6784 (tpp80) cc_final: 0.6318 (tpp80) REVERT: E 492 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6498 (tm-30) REVERT: F 81 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7609 (mp0) REVERT: F 166 TRP cc_start: 0.8143 (t-100) cc_final: 0.7836 (t-100) REVERT: F 227 PHE cc_start: 0.8303 (m-80) cc_final: 0.8042 (m-10) REVERT: F 240 SER cc_start: 0.8792 (m) cc_final: 0.8397 (t) REVERT: F 398 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: G 240 SER cc_start: 0.8849 (m) cc_final: 0.8465 (t) REVERT: G 334 LEU cc_start: 0.8830 (mm) cc_final: 0.7740 (tp) REVERT: G 398 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8913 (m-10) REVERT: H 240 SER cc_start: 0.8792 (m) cc_final: 0.8443 (t) REVERT: H 334 LEU cc_start: 0.8815 (mm) cc_final: 0.8401 (mm) REVERT: H 492 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6744 (tm-30) REVERT: H 646 MET cc_start: 0.6655 (ptt) cc_final: 0.6309 (ptt) REVERT: H 685 MET cc_start: 0.6923 (tpt) cc_final: 0.6659 (tpt) REVERT: I 240 SER cc_start: 0.8902 (m) cc_final: 0.8489 (t) REVERT: I 492 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6779 (tm-30) REVERT: J 81 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7562 (mp0) REVERT: J 104 ILE cc_start: 0.8816 (mt) cc_final: 0.8548 (mt) REVERT: J 166 TRP cc_start: 0.8165 (t-100) cc_final: 0.7763 (t-100) REVERT: J 371 ARG cc_start: 0.6783 (tpp80) cc_final: 0.6318 (tpp80) REVERT: J 492 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6496 (tm-30) outliers start: 278 outliers final: 214 residues processed: 1190 average time/residue: 0.5438 time to fit residues: 1102.4558 Evaluate side-chains 1173 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 954 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 420 ASN Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 693 ILE Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 555 LEU Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 664 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 420 ASN Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 693 ILE Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 526 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 243 optimal weight: 3.9990 chunk 652 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 425 optimal weight: 0.0870 chunk 178 optimal weight: 5.9990 chunk 725 optimal weight: 8.9990 chunk 602 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 380 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 262 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 262 ASN ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 ASN ** I 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 ASN ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 58550 Z= 0.267 Angle : 0.707 11.668 79640 Z= 0.351 Chirality : 0.046 0.214 8900 Planarity : 0.005 0.077 10360 Dihedral : 6.972 54.914 8162 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 5.44 % Allowed : 27.14 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.09), residues: 7470 helix: -2.15 (0.09), residues: 2760 sheet: -3.14 (0.14), residues: 840 loop : -2.89 (0.09), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 247 HIS 0.005 0.001 HIS A 392 PHE 0.015 0.001 PHE J 364 TYR 0.029 0.002 TYR G 359 ARG 0.013 0.000 ARG J 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 983 time to evaluate : 4.795 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: symmetry clash REVERT: A 240 SER cc_start: 0.8783 (m) cc_final: 0.8393 (t) REVERT: A 398 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8924 (m-80) REVERT: B 240 SER cc_start: 0.8872 (m) cc_final: 0.8505 (t) REVERT: B 334 LEU cc_start: 0.8855 (mm) cc_final: 0.7819 (tp) REVERT: B 398 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8958 (m-10) REVERT: B 439 LEU cc_start: 0.9383 (tp) cc_final: 0.9094 (tp) REVERT: B 522 LEU cc_start: 0.8251 (pt) cc_final: 0.7675 (pp) REVERT: C 166 TRP cc_start: 0.8282 (t-100) cc_final: 0.7794 (t-100) REVERT: C 240 SER cc_start: 0.8804 (m) cc_final: 0.8500 (t) REVERT: C 334 LEU cc_start: 0.8848 (mm) cc_final: 0.7898 (tp) REVERT: C 492 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6736 (tm-30) REVERT: D 220 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6965 (mt-10) REVERT: D 240 SER cc_start: 0.8903 (m) cc_final: 0.8520 (t) REVERT: D 492 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6763 (tm-30) REVERT: E 104 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8585 (mt) REVERT: E 227 PHE cc_start: 0.8409 (m-80) cc_final: 0.8080 (m-80) REVERT: E 492 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6489 (tm-30) REVERT: F 240 SER cc_start: 0.8794 (m) cc_final: 0.8407 (t) REVERT: F 398 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: G 240 SER cc_start: 0.8881 (m) cc_final: 0.8514 (t) REVERT: G 334 LEU cc_start: 0.8856 (mm) cc_final: 0.7818 (tp) REVERT: G 398 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8955 (m-10) REVERT: G 439 LEU cc_start: 0.9387 (tp) cc_final: 0.9101 (tp) REVERT: G 522 LEU cc_start: 0.8245 (pt) cc_final: 0.7666 (pp) REVERT: H 166 TRP cc_start: 0.8286 (t-100) cc_final: 0.7798 (t-100) REVERT: H 240 SER cc_start: 0.8813 (m) cc_final: 0.8500 (t) REVERT: H 273 MET cc_start: 0.7302 (mpp) cc_final: 0.6754 (mmt) REVERT: H 334 LEU cc_start: 0.8854 (mm) cc_final: 0.7888 (tp) REVERT: H 492 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6744 (tm-30) REVERT: I 240 SER cc_start: 0.8917 (m) cc_final: 0.8539 (t) REVERT: I 492 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6766 (tm-30) REVERT: J 104 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8589 (mt) REVERT: J 227 PHE cc_start: 0.8405 (m-80) cc_final: 0.8074 (m-80) REVERT: J 492 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6490 (tm-30) outliers start: 316 outliers final: 262 residues processed: 1170 average time/residue: 0.5248 time to fit residues: 1052.5638 Evaluate side-chains 1209 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 941 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 359 TYR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 693 ILE Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain F residue 729 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 693 ILE Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 697 MET Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 664 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 385 VAL Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 526 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 699 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 chunk 529 optimal weight: 9.9990 chunk 410 optimal weight: 5.9990 chunk 610 optimal weight: 10.0000 chunk 405 optimal weight: 9.9990 chunk 722 optimal weight: 0.8980 chunk 452 optimal weight: 0.9990 chunk 440 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 343 GLN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 343 GLN ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 ASN ** F 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 58550 Z= 0.386 Angle : 0.775 11.054 79640 Z= 0.388 Chirality : 0.048 0.220 8900 Planarity : 0.006 0.078 10360 Dihedral : 7.295 61.173 8162 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.79 % Favored : 83.21 % Rotamer: Outliers : 6.11 % Allowed : 27.11 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.09), residues: 7470 helix: -2.10 (0.09), residues: 2700 sheet: -3.37 (0.14), residues: 850 loop : -2.89 (0.09), residues: 3920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 583 HIS 0.004 0.001 HIS I 389 PHE 0.017 0.002 PHE D 570 TYR 0.037 0.003 TYR J 359 ARG 0.011 0.000 ARG J 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 950 time to evaluate : 4.785 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: A 240 SER cc_start: 0.8865 (m) cc_final: 0.8533 (t) REVERT: A 398 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8969 (m-80) REVERT: B 166 TRP cc_start: 0.8439 (t-100) cc_final: 0.8101 (t-100) REVERT: B 240 SER cc_start: 0.8893 (m) cc_final: 0.8551 (t) REVERT: B 334 LEU cc_start: 0.8779 (mm) cc_final: 0.7769 (tp) REVERT: B 398 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8994 (m-10) REVERT: C 166 TRP cc_start: 0.8349 (t-100) cc_final: 0.7566 (t-100) REVERT: C 240 SER cc_start: 0.8873 (m) cc_final: 0.8587 (t) REVERT: C 492 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6719 (tm-30) REVERT: D 220 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7063 (mt-10) REVERT: D 240 SER cc_start: 0.8939 (m) cc_final: 0.8582 (t) REVERT: D 424 MET cc_start: 0.8086 (mmm) cc_final: 0.7857 (mmt) REVERT: E 104 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8603 (mt) REVERT: E 492 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6452 (tm-30) REVERT: F 240 SER cc_start: 0.8886 (m) cc_final: 0.8546 (t) REVERT: F 398 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: G 166 TRP cc_start: 0.8439 (t-100) cc_final: 0.8101 (t-100) REVERT: G 240 SER cc_start: 0.8902 (m) cc_final: 0.8569 (t) REVERT: G 334 LEU cc_start: 0.8782 (mm) cc_final: 0.7769 (tp) REVERT: G 398 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8993 (m-10) REVERT: H 166 TRP cc_start: 0.8350 (t-100) cc_final: 0.7570 (t-100) REVERT: H 240 SER cc_start: 0.8881 (m) cc_final: 0.8579 (t) REVERT: H 334 LEU cc_start: 0.8854 (mm) cc_final: 0.7889 (tp) REVERT: H 440 ASP cc_start: 0.7964 (t0) cc_final: 0.7760 (t0) REVERT: H 492 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6718 (tm-30) REVERT: I 240 SER cc_start: 0.8950 (m) cc_final: 0.8593 (t) REVERT: I 424 MET cc_start: 0.8065 (mmm) cc_final: 0.7848 (mmt) REVERT: J 104 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8606 (mt) REVERT: J 492 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6448 (tm-30) outliers start: 355 outliers final: 290 residues processed: 1170 average time/residue: 0.5172 time to fit residues: 1046.1272 Evaluate side-chains 1220 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 924 time to evaluate : 4.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 398 PHE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 420 ASN Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 729 ASP Chi-restraints excluded: chain F residue 745 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 569 SER Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 684 VAL Chi-restraints excluded: chain G residue 693 ILE Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 569 SER Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 664 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 112 MET Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 522 LEU Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 729 ASP Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 385 VAL Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 428 SER Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 447 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 431 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 459 optimal weight: 0.5980 chunk 492 optimal weight: 0.7980 chunk 357 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 568 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 ASN ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN ** F 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 GLN ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 420 ASN ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58550 Z= 0.183 Angle : 0.684 10.651 79640 Z= 0.336 Chirality : 0.044 0.221 8900 Planarity : 0.005 0.075 10360 Dihedral : 6.800 59.767 8160 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 4.89 % Allowed : 28.80 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.09), residues: 7470 helix: -2.00 (0.09), residues: 2770 sheet: -3.15 (0.14), residues: 850 loop : -2.84 (0.09), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 583 HIS 0.006 0.001 HIS F 212 PHE 0.015 0.001 PHE D 570 TYR 0.024 0.002 TYR J 359 ARG 0.008 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1048 time to evaluate : 5.355 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: A 166 TRP cc_start: 0.8156 (t-100) cc_final: 0.7930 (t-100) REVERT: A 239 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7661 (p) REVERT: A 240 SER cc_start: 0.8815 (m) cc_final: 0.8465 (t) REVERT: A 398 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8873 (m-80) REVERT: A 521 VAL cc_start: 0.8797 (t) cc_final: 0.8571 (p) REVERT: B 239 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7622 (p) REVERT: B 240 SER cc_start: 0.8830 (m) cc_final: 0.8491 (t) REVERT: B 294 ILE cc_start: 0.7796 (tt) cc_final: 0.7560 (tt) REVERT: B 334 LEU cc_start: 0.8722 (mm) cc_final: 0.7785 (tp) REVERT: B 398 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8888 (m-10) REVERT: B 558 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7157 (mtt90) REVERT: C 239 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7676 (p) REVERT: C 240 SER cc_start: 0.8816 (m) cc_final: 0.8545 (t) REVERT: C 248 HIS cc_start: 0.6923 (t-90) cc_final: 0.6654 (t-90) REVERT: C 334 LEU cc_start: 0.8800 (mm) cc_final: 0.7817 (tp) REVERT: C 492 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6690 (tm-30) REVERT: C 519 ASP cc_start: 0.6680 (t0) cc_final: 0.5970 (t70) REVERT: C 558 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7392 (mtt90) REVERT: D 192 GLU cc_start: 0.6650 (mp0) cc_final: 0.6412 (mp0) REVERT: D 220 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6973 (mt-10) REVERT: D 239 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7631 (p) REVERT: D 240 SER cc_start: 0.8820 (m) cc_final: 0.8514 (t) REVERT: E 104 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8560 (mt) REVERT: E 227 PHE cc_start: 0.8368 (m-80) cc_final: 0.7995 (m-80) REVERT: E 334 LEU cc_start: 0.8513 (mm) cc_final: 0.8233 (mm) REVERT: E 477 ASP cc_start: 0.5015 (OUTLIER) cc_final: 0.4812 (m-30) REVERT: E 492 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6473 (tm-30) REVERT: F 166 TRP cc_start: 0.8163 (t-100) cc_final: 0.7930 (t-100) REVERT: F 227 PHE cc_start: 0.8305 (m-80) cc_final: 0.7895 (m-10) REVERT: F 239 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7634 (p) REVERT: F 240 SER cc_start: 0.8855 (m) cc_final: 0.8483 (t) REVERT: F 398 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: F 521 VAL cc_start: 0.8803 (t) cc_final: 0.8575 (p) REVERT: G 239 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7635 (p) REVERT: G 240 SER cc_start: 0.8839 (m) cc_final: 0.8501 (t) REVERT: G 294 ILE cc_start: 0.7792 (tt) cc_final: 0.7562 (tt) REVERT: G 334 LEU cc_start: 0.8683 (mm) cc_final: 0.7737 (tp) REVERT: G 398 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8885 (m-10) REVERT: G 558 ARG cc_start: 0.8010 (mmt-90) cc_final: 0.7157 (mtt90) REVERT: H 240 SER cc_start: 0.8808 (m) cc_final: 0.8465 (t) REVERT: H 248 HIS cc_start: 0.6876 (t-90) cc_final: 0.6576 (t-90) REVERT: H 273 MET cc_start: 0.7152 (mpp) cc_final: 0.6656 (mmt) REVERT: H 285 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6966 (mtm180) REVERT: H 334 LEU cc_start: 0.8822 (mm) cc_final: 0.7919 (tp) REVERT: H 492 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6696 (tm-30) REVERT: H 519 ASP cc_start: 0.6605 (t0) cc_final: 0.5886 (t0) REVERT: H 558 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7388 (mtt90) REVERT: I 240 SER cc_start: 0.8871 (m) cc_final: 0.8490 (t) REVERT: J 104 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (mt) REVERT: J 227 PHE cc_start: 0.8364 (m-80) cc_final: 0.7991 (m-80) REVERT: J 334 LEU cc_start: 0.8510 (mm) cc_final: 0.8234 (mm) REVERT: J 477 ASP cc_start: 0.5018 (OUTLIER) cc_final: 0.4814 (m-30) REVERT: J 492 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6442 (tm-30) outliers start: 284 outliers final: 222 residues processed: 1221 average time/residue: 0.5335 time to fit residues: 1116.9570 Evaluate side-chains 1221 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 984 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 420 ASN Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 420 ASN Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 693 ILE Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 729 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 658 SER Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 693 ILE Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 555 LEU Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 664 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 421 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 664 LEU Chi-restraints excluded: chain I residue 693 ILE Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 385 VAL Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 420 ASN Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 428 SER Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 477 ASP Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 526 ILE Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 657 optimal weight: 0.5980 chunk 692 optimal weight: 6.9990 chunk 631 optimal weight: 0.3980 chunk 673 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 293 optimal weight: 8.9990 chunk 528 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 608 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 671 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 262 ASN A 343 GLN A 420 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS F 343 GLN ** F 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 GLN ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 58550 Z= 0.306 Angle : 0.742 10.348 79640 Z= 0.368 Chirality : 0.047 0.204 8900 Planarity : 0.006 0.106 10360 Dihedral : 6.978 64.425 8160 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer: Outliers : 5.22 % Allowed : 29.05 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.09), residues: 7470 helix: -1.92 (0.09), residues: 2710 sheet: -3.10 (0.14), residues: 830 loop : -2.78 (0.10), residues: 3930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 583 HIS 0.005 0.001 HIS D 231 PHE 0.041 0.002 PHE G 364 TYR 0.038 0.002 TYR B 359 ARG 0.014 0.000 ARG I 676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 972 time to evaluate : 4.879 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 166 TRP cc_start: 0.8258 (t-100) cc_final: 0.7923 (t-100) REVERT: A 240 SER cc_start: 0.8869 (m) cc_final: 0.8490 (t) REVERT: A 398 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8930 (m-80) REVERT: A 521 VAL cc_start: 0.8839 (t) cc_final: 0.8602 (p) REVERT: A 522 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8259 (pp) REVERT: B 166 TRP cc_start: 0.8369 (t-100) cc_final: 0.8026 (t-100) REVERT: B 240 SER cc_start: 0.8909 (m) cc_final: 0.8544 (t) REVERT: B 334 LEU cc_start: 0.8740 (mm) cc_final: 0.7735 (tp) REVERT: B 341 ILE cc_start: 0.7764 (mm) cc_final: 0.7560 (mm) REVERT: B 398 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8990 (m-10) REVERT: C 240 SER cc_start: 0.8868 (m) cc_final: 0.8578 (t) REVERT: C 285 ARG cc_start: 0.7171 (mtm180) cc_final: 0.6949 (mtm180) REVERT: C 492 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 519 ASP cc_start: 0.6666 (t0) cc_final: 0.5988 (t0) REVERT: C 697 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6050 (ptt) REVERT: D 166 TRP cc_start: 0.8247 (t-100) cc_final: 0.7697 (t-100) REVERT: D 240 SER cc_start: 0.8910 (m) cc_final: 0.8558 (t) REVERT: D 339 GLU cc_start: 0.6250 (tp30) cc_final: 0.6050 (tp30) REVERT: D 486 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.6964 (t60) REVERT: E 81 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7569 (mp0) REVERT: E 486 TRP cc_start: 0.7446 (OUTLIER) cc_final: 0.7089 (t60) REVERT: E 492 GLU cc_start: 0.6674 (tm-30) cc_final: 0.6447 (tm-30) REVERT: F 166 TRP cc_start: 0.8266 (t-100) cc_final: 0.7924 (t-100) REVERT: F 240 SER cc_start: 0.8857 (m) cc_final: 0.8492 (t) REVERT: F 398 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: F 521 VAL cc_start: 0.8838 (t) cc_final: 0.8600 (p) REVERT: F 522 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8261 (pp) REVERT: G 166 TRP cc_start: 0.8366 (t-100) cc_final: 0.8022 (t-100) REVERT: G 240 SER cc_start: 0.8916 (m) cc_final: 0.8554 (t) REVERT: G 334 LEU cc_start: 0.8727 (mm) cc_final: 0.7709 (tp) REVERT: G 341 ILE cc_start: 0.7769 (mm) cc_final: 0.7562 (mm) REVERT: G 398 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8987 (m-10) REVERT: G 492 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6616 (tm-30) REVERT: H 240 SER cc_start: 0.8855 (m) cc_final: 0.8564 (t) REVERT: H 273 MET cc_start: 0.7099 (mpp) cc_final: 0.6643 (mmp) REVERT: H 334 LEU cc_start: 0.8840 (mm) cc_final: 0.7923 (tp) REVERT: H 492 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6735 (tm-30) REVERT: H 697 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6055 (ptt) REVERT: I 166 TRP cc_start: 0.8248 (t-100) cc_final: 0.7698 (t-100) REVERT: I 240 SER cc_start: 0.8918 (m) cc_final: 0.8585 (t) REVERT: I 339 GLU cc_start: 0.6256 (tp30) cc_final: 0.6052 (tp30) REVERT: I 486 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.6970 (t60) REVERT: J 81 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7551 (mp0) REVERT: J 486 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.7096 (t60) REVERT: J 492 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6449 (tm-30) outliers start: 303 outliers final: 237 residues processed: 1154 average time/residue: 0.5328 time to fit residues: 1056.0778 Evaluate side-chains 1212 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 963 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 359 TYR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 486 TRP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 486 TRP Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 565 THR Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 693 ILE Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 729 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 658 SER Chi-restraints excluded: chain G residue 664 LEU Chi-restraints excluded: chain G residue 684 VAL Chi-restraints excluded: chain G residue 693 ILE Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain H residue 697 MET Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 359 TYR Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 421 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 486 TRP Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 693 ILE Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 729 ASP Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 385 VAL Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 402 SER Chi-restraints excluded: chain J residue 428 SER Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 486 TRP Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 569 SER Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 696 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 442 optimal weight: 0.9980 chunk 712 optimal weight: 1.9990 chunk 434 optimal weight: 8.9990 chunk 337 optimal weight: 9.9990 chunk 495 optimal weight: 0.8980 chunk 747 optimal weight: 0.7980 chunk 687 optimal weight: 5.9990 chunk 594 optimal weight: 1.9990 chunk 61 optimal weight: 50.0000 chunk 459 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 420 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 58550 Z= 0.200 Angle : 0.706 11.742 79640 Z= 0.345 Chirality : 0.045 0.326 8900 Planarity : 0.005 0.078 10360 Dihedral : 6.727 65.388 8160 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 4.39 % Allowed : 30.10 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.09), residues: 7470 helix: -1.93 (0.09), residues: 2770 sheet: -2.99 (0.15), residues: 850 loop : -2.77 (0.09), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 583 HIS 0.005 0.001 HIS D 392 PHE 0.034 0.001 PHE B 364 TYR 0.036 0.002 TYR G 359 ARG 0.014 0.000 ARG D 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14940 Ramachandran restraints generated. 7470 Oldfield, 0 Emsley, 7470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1013 time to evaluate : 4.797 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 166 TRP cc_start: 0.8149 (t-100) cc_final: 0.7933 (t-100) REVERT: A 239 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7603 (p) REVERT: A 240 SER cc_start: 0.8852 (m) cc_final: 0.8558 (t) REVERT: A 398 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: A 439 LEU cc_start: 0.9142 (mt) cc_final: 0.8928 (mt) REVERT: A 521 VAL cc_start: 0.8768 (t) cc_final: 0.8527 (p) REVERT: A 691 PRO cc_start: 0.7881 (Cg_exo) cc_final: 0.7594 (Cg_endo) REVERT: B 239 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7568 (p) REVERT: B 240 SER cc_start: 0.8849 (m) cc_final: 0.8545 (t) REVERT: B 341 ILE cc_start: 0.7696 (mm) cc_final: 0.7464 (mm) REVERT: B 398 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8912 (m-10) REVERT: B 558 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7136 (mtt90) REVERT: C 240 SER cc_start: 0.8879 (m) cc_final: 0.8513 (t) REVERT: C 334 LEU cc_start: 0.8704 (mm) cc_final: 0.7782 (tp) REVERT: C 492 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6703 (tm-30) REVERT: C 519 ASP cc_start: 0.6660 (t0) cc_final: 0.5968 (t0) REVERT: C 558 ARG cc_start: 0.7937 (mmt-90) cc_final: 0.7447 (mtt90) REVERT: C 697 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6014 (ptt) REVERT: D 81 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7674 (mp0) REVERT: D 239 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7598 (p) REVERT: D 240 SER cc_start: 0.8877 (m) cc_final: 0.8579 (t) REVERT: E 81 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7548 (mp0) REVERT: E 166 TRP cc_start: 0.8276 (t-100) cc_final: 0.7860 (t-100) REVERT: E 486 TRP cc_start: 0.7360 (OUTLIER) cc_final: 0.7046 (t60) REVERT: E 492 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6492 (tm-30) REVERT: E 521 VAL cc_start: 0.8489 (m) cc_final: 0.8182 (p) REVERT: F 166 TRP cc_start: 0.8147 (t-100) cc_final: 0.7925 (t-100) REVERT: F 240 SER cc_start: 0.8851 (m) cc_final: 0.8463 (t) REVERT: F 398 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: F 439 LEU cc_start: 0.9139 (mt) cc_final: 0.8924 (mt) REVERT: F 521 VAL cc_start: 0.8771 (t) cc_final: 0.8528 (p) REVERT: F 691 PRO cc_start: 0.7876 (Cg_exo) cc_final: 0.7598 (Cg_endo) REVERT: G 239 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7589 (p) REVERT: G 240 SER cc_start: 0.8858 (m) cc_final: 0.8557 (t) REVERT: G 341 ILE cc_start: 0.7701 (mm) cc_final: 0.7468 (mm) REVERT: G 398 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8917 (m-10) REVERT: G 558 ARG cc_start: 0.8008 (mmt-90) cc_final: 0.7140 (mtt90) REVERT: H 239 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7674 (p) REVERT: H 240 SER cc_start: 0.8843 (m) cc_final: 0.8588 (t) REVERT: H 273 MET cc_start: 0.7087 (mpp) cc_final: 0.6603 (mmp) REVERT: H 285 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.7011 (mtm180) REVERT: H 420 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7473 (t0) REVERT: H 492 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6712 (tm-30) REVERT: H 519 ASP cc_start: 0.6673 (t0) cc_final: 0.5956 (t0) REVERT: H 558 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7445 (mtt90) REVERT: H 697 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6017 (ptt) REVERT: I 81 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7668 (mp0) REVERT: I 240 SER cc_start: 0.8893 (m) cc_final: 0.8544 (t) REVERT: J 81 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7526 (mp0) REVERT: J 166 TRP cc_start: 0.8277 (t-100) cc_final: 0.7861 (t-100) REVERT: J 227 PHE cc_start: 0.8325 (m-80) cc_final: 0.7987 (m-80) REVERT: J 486 TRP cc_start: 0.7345 (OUTLIER) cc_final: 0.7033 (t60) REVERT: J 492 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6495 (tm-30) REVERT: J 521 VAL cc_start: 0.8491 (m) cc_final: 0.8186 (p) outliers start: 255 outliers final: 225 residues processed: 1170 average time/residue: 0.5287 time to fit residues: 1066.2568 Evaluate side-chains 1191 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 951 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 398 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 745 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 486 TRP Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 569 SER Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 623 LEU Chi-restraints excluded: chain E residue 664 LEU Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 729 ASP Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain F residue 402 SER Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 458 THR Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 623 LEU Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 693 ILE Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 729 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 248 HIS Chi-restraints excluded: chain G residue 296 LEU Chi-restraints excluded: chain G residue 303 SER Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 398 PHE Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 428 SER Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 494 THR Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 579 THR Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain G residue 658 SER Chi-restraints excluded: chain G residue 684 VAL Chi-restraints excluded: chain G residue 693 ILE Chi-restraints excluded: chain G residue 696 ILE Chi-restraints excluded: chain G residue 745 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 231 HIS Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 303 SER Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 420 ASN Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 455 ILE Chi-restraints excluded: chain H residue 494 THR Chi-restraints excluded: chain H residue 526 ILE Chi-restraints excluded: chain H residue 623 LEU Chi-restraints excluded: chain H residue 693 ILE Chi-restraints excluded: chain H residue 696 ILE Chi-restraints excluded: chain H residue 697 MET Chi-restraints excluded: chain H residue 729 ASP Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 231 HIS Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 303 SER Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 402 SER Chi-restraints excluded: chain I residue 421 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 579 THR Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 693 ILE Chi-restraints excluded: chain I residue 696 ILE Chi-restraints excluded: chain I residue 745 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain J residue 201 VAL Chi-restraints excluded: chain J residue 231 HIS Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 344 THR Chi-restraints excluded: chain J residue 385 VAL Chi-restraints excluded: chain J residue 398 PHE Chi-restraints excluded: chain J residue 428 SER Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 486 TRP Chi-restraints excluded: chain J residue 494 THR Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 569 SER Chi-restraints excluded: chain J residue 579 THR Chi-restraints excluded: chain J residue 623 LEU Chi-restraints excluded: chain J residue 664 LEU Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 696 ILE Chi-restraints excluded: chain J residue 729 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 472 optimal weight: 7.9990 chunk 633 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 548 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 595 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 611 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** F 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 ASN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 420 ASN ** H 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.204457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.173641 restraints weight = 76138.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177523 restraints weight = 49149.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.180151 restraints weight = 36449.168| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 58550 Z= 0.287 Angle : 0.735 11.395 79640 Z= 0.363 Chirality : 0.047 0.338 8900 Planarity : 0.006 0.089 10360 Dihedral : 6.842 68.370 8160 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.27 % Favored : 84.73 % Rotamer: Outliers : 4.70 % Allowed : 30.17 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.09), residues: 7470 helix: -1.94 (0.09), residues: 2780 sheet: -2.93 (0.15), residues: 830 loop : -2.77 (0.10), residues: 3860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 583 HIS 0.005 0.001 HIS I 231 PHE 0.035 0.002 PHE B 364 TYR 0.036 0.002 TYR G 359 ARG 0.014 0.000 ARG D 676 =============================================================================== Job complete usr+sys time: 15940.43 seconds wall clock time: 279 minutes 24.99 seconds (16764.99 seconds total)