Starting phenix.real_space_refine on Mon Mar 18 13:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/03_2024/6sh3_10192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/03_2024/6sh3_10192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/03_2024/6sh3_10192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/03_2024/6sh3_10192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/03_2024/6sh3_10192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/03_2024/6sh3_10192_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 14 5.49 5 S 112 5.16 5 C 13412 2.51 5 N 3584 2.21 5 O 3899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 405": "OE1" <-> "OE2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 200": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G GLU 312": "OE1" <-> "OE2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G GLU 405": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21021 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.30, per 1000 atoms: 0.54 Number of scatterers: 21021 At special positions: 0 Unit cell: (157.791, 155.673, 132.375, 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 112 16.00 P 14 15.00 O 3899 8.00 N 3584 7.00 C 13412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.55 Conformation dependent library (CDL) restraints added in 3.9 seconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 28 sheets defined 39.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 4.853A pdb=" N HIS A 182 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 185 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.640A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 239' Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.818A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.866A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 198 removed outlier: 4.853A pdb=" N HIS B 182 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP B 185 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 198 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.640A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 239' Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.818A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.866A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 198 removed outlier: 4.853A pdb=" N HIS C 182 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP C 185 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 198 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.639A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 239' Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.818A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.866A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 82 removed outlier: 3.835A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 198 removed outlier: 4.852A pdb=" N HIS D 182 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP D 185 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS D 197 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 198 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.640A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 239' Processing helix chain 'D' and resid 241 through 245 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 300 through 308 removed outlier: 3.817A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 342 through 350 Processing helix chain 'D' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU D 395 " --> pdb=" O PRO D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.865A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 198 removed outlier: 4.852A pdb=" N HIS E 182 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP E 185 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR E 198 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.639A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 239' Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 300 through 308 removed outlier: 3.819A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 342 through 350 Processing helix chain 'E' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 411 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER E 415 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.866A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 82 removed outlier: 3.835A pdb=" N GLY F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 105 removed outlier: 3.516A pdb=" N LYS F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 198 removed outlier: 4.853A pdb=" N HIS F 182 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP F 185 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS F 197 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 198 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 227 No H-bonds generated for 'chain 'F' and resid 225 through 227' Processing helix chain 'F' and resid 234 through 239 removed outlier: 3.639A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 239' Processing helix chain 'F' and resid 241 through 245 Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 300 through 308 removed outlier: 3.818A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 323 No H-bonds generated for 'chain 'F' and resid 321 through 323' Processing helix chain 'F' and resid 342 through 350 Processing helix chain 'F' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU F 395 " --> pdb=" O PRO F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 411 " --> pdb=" O ASP F 407 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.866A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL G 78 " --> pdb=" O LYS G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 198 removed outlier: 4.853A pdb=" N HIS G 182 " --> pdb=" O ARG G 179 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP G 185 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS G 197 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 198 " --> pdb=" O ALA G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 227 No H-bonds generated for 'chain 'G' and resid 225 through 227' Processing helix chain 'G' and resid 234 through 239 removed outlier: 3.639A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 239 " --> pdb=" O LYS G 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 234 through 239' Processing helix chain 'G' and resid 241 through 245 Processing helix chain 'G' and resid 249 through 254 Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 300 through 308 removed outlier: 3.819A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 323 No H-bonds generated for 'chain 'G' and resid 321 through 323' Processing helix chain 'G' and resid 342 through 350 Processing helix chain 'G' and resid 391 through 401 removed outlier: 3.522A pdb=" N GLU G 395 " --> pdb=" O PRO G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 416 removed outlier: 3.915A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS G 411 " --> pdb=" O ASP G 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 433 Processing helix chain 'G' and resid 439 through 445 removed outlier: 3.866A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.569A pdb=" N ILE A 152 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 115 through 122 Processing sheet with id= C, first strand: chain 'A' and resid 205 through 208 removed outlier: 4.335A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 383 through 385 removed outlier: 8.868A pdb=" N VAL A 384 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 264 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR A 358 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR A 263 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 360 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 265 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET A 362 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER A 314 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE A 361 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 316 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR A 363 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 318 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.570A pdb=" N ILE B 152 " --> pdb=" O HIS B 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 115 through 122 Processing sheet with id= G, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.335A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 383 through 385 removed outlier: 8.868A pdb=" N VAL B 384 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 264 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR B 358 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR B 263 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR B 360 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 265 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET B 362 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER B 314 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N PHE B 361 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 316 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR B 363 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 318 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.570A pdb=" N ILE C 152 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 115 through 122 Processing sheet with id= K, first strand: chain 'C' and resid 205 through 208 removed outlier: 4.336A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 383 through 385 removed outlier: 8.868A pdb=" N VAL C 384 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 264 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR C 358 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR C 263 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 360 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU C 265 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET C 362 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER C 314 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE C 361 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 316 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR C 363 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 318 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.569A pdb=" N ILE D 152 " --> pdb=" O HIS D 141 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 115 through 122 Processing sheet with id= O, first strand: chain 'D' and resid 205 through 208 removed outlier: 4.335A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 383 through 385 removed outlier: 8.868A pdb=" N VAL D 384 " --> pdb=" O GLY D 262 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 264 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 358 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR D 263 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 360 " --> pdb=" O TYR D 263 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU D 265 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET D 362 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER D 314 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE D 361 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 316 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR D 363 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU D 318 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.569A pdb=" N ILE E 152 " --> pdb=" O HIS E 141 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 115 through 122 Processing sheet with id= S, first strand: chain 'E' and resid 205 through 208 removed outlier: 4.335A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 383 through 385 removed outlier: 8.869A pdb=" N VAL E 384 " --> pdb=" O GLY E 262 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E 264 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR E 358 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR E 263 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR E 360 " --> pdb=" O TYR E 263 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU E 265 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET E 362 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER E 314 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N PHE E 361 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU E 316 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR E 363 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU E 318 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.569A pdb=" N ILE F 152 " --> pdb=" O HIS F 141 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 115 through 122 Processing sheet with id= W, first strand: chain 'F' and resid 205 through 208 removed outlier: 4.334A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 383 through 385 removed outlier: 8.869A pdb=" N VAL F 384 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU F 264 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR F 358 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR F 263 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR F 360 " --> pdb=" O TYR F 263 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU F 265 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET F 362 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER F 314 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE F 361 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU F 316 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR F 363 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU F 318 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 87 through 90 removed outlier: 3.569A pdb=" N ILE G 152 " --> pdb=" O HIS G 141 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 115 through 122 Processing sheet with id= AA, first strand: chain 'G' and resid 205 through 208 removed outlier: 4.335A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 383 through 385 removed outlier: 8.868A pdb=" N VAL G 384 " --> pdb=" O GLY G 262 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU G 264 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR G 358 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR G 263 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR G 360 " --> pdb=" O TYR G 263 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU G 265 " --> pdb=" O THR G 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET G 362 " --> pdb=" O LEU G 265 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER G 314 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE G 361 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU G 316 " --> pdb=" O PHE G 361 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR G 363 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU G 318 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB 700 hydrogen bonds defined for protein. 1722 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: 6.20 Time building geometry restraints manager: 9.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6589 1.34 - 1.46: 3931 1.46 - 1.57: 10725 1.57 - 1.69: 21 1.69 - 1.81: 210 Bond restraints: 21476 Sorted by residual: bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 21471 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.66: 720 106.66 - 113.52: 11697 113.52 - 120.38: 8204 120.38 - 127.24: 8176 127.24 - 134.10: 232 Bond angle restraints: 29029 Sorted by residual: angle pdb=" N PRO G 403 " pdb=" CA PRO G 403 " pdb=" CB PRO G 403 " ideal model delta sigma weight residual 103.31 110.36 -7.05 8.90e-01 1.26e+00 6.28e+01 angle pdb=" N PRO D 403 " pdb=" CA PRO D 403 " pdb=" CB PRO D 403 " ideal model delta sigma weight residual 103.31 110.34 -7.03 8.90e-01 1.26e+00 6.25e+01 angle pdb=" N PRO B 403 " pdb=" CA PRO B 403 " pdb=" CB PRO B 403 " ideal model delta sigma weight residual 103.31 110.32 -7.01 8.90e-01 1.26e+00 6.21e+01 angle pdb=" N PRO E 403 " pdb=" CA PRO E 403 " pdb=" CB PRO E 403 " ideal model delta sigma weight residual 103.31 110.32 -7.01 8.90e-01 1.26e+00 6.21e+01 angle pdb=" N PRO F 403 " pdb=" CA PRO F 403 " pdb=" CB PRO F 403 " ideal model delta sigma weight residual 103.31 110.32 -7.01 8.90e-01 1.26e+00 6.20e+01 ... (remaining 29024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 11631 16.92 - 33.85: 996 33.85 - 50.77: 148 50.77 - 67.70: 47 67.70 - 84.62: 16 Dihedral angle restraints: 12838 sinusoidal: 5264 harmonic: 7574 Sorted by residual: dihedral pdb=" CA GLN G 218 " pdb=" C GLN G 218 " pdb=" N PRO G 219 " pdb=" CA PRO G 219 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN E 218 " pdb=" C GLN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN F 218 " pdb=" C GLN F 218 " pdb=" N PRO F 219 " pdb=" CA PRO F 219 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2178 0.046 - 0.093: 769 0.093 - 0.139: 171 0.139 - 0.185: 67 0.185 - 0.232: 28 Chirality restraints: 3213 Sorted by residual: chirality pdb=" CA ASP E 285 " pdb=" N ASP E 285 " pdb=" C ASP E 285 " pdb=" CB ASP E 285 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP B 285 " pdb=" N ASP B 285 " pdb=" C ASP B 285 " pdb=" CB ASP B 285 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP G 285 " pdb=" N ASP G 285 " pdb=" C ASP G 285 " pdb=" CB ASP G 285 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3210 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 74 " 0.023 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C LYS B 74 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS B 74 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA B 75 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 74 " -0.023 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C LYS E 74 " 0.077 2.00e-02 2.50e+03 pdb=" O LYS E 74 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA E 75 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 74 " -0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C LYS G 74 " 0.076 2.00e-02 2.50e+03 pdb=" O LYS G 74 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA G 75 " -0.026 2.00e-02 2.50e+03 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5923 2.81 - 3.33: 19243 3.33 - 3.85: 32510 3.85 - 4.38: 38259 4.38 - 4.90: 65353 Nonbonded interactions: 161288 Sorted by model distance: nonbonded pdb=" O PHE E 412 " pdb=" OG SER E 415 " model vdw 2.287 2.440 nonbonded pdb=" O PHE B 412 " pdb=" OG SER B 415 " model vdw 2.287 2.440 nonbonded pdb=" O PHE A 412 " pdb=" OG SER A 415 " model vdw 2.287 2.440 nonbonded pdb=" O PHE C 412 " pdb=" OG SER C 415 " model vdw 2.287 2.440 nonbonded pdb=" O PHE D 412 " pdb=" OG SER D 415 " model vdw 2.288 2.440 ... (remaining 161283 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.020 Extract box with map and model: 4.720 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 57.060 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.006 0.110 21476 Z= 0.392 Angle : 0.912 10.861 29029 Z= 0.494 Chirality : 0.053 0.232 3213 Planarity : 0.007 0.067 3640 Dihedral : 13.400 84.622 7980 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.62 % Allowed : 5.88 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.15), residues: 2576 helix: -1.02 (0.14), residues: 1036 sheet: -2.90 (0.17), residues: 651 loop : -2.76 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 102 HIS 0.002 0.001 HIS B 123 PHE 0.009 0.001 PHE D 276 TYR 0.031 0.002 TYR D 259 ARG 0.014 0.001 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 397 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8813 (mm) cc_final: 0.8422 (mm) REVERT: A 119 ASN cc_start: 0.7560 (p0) cc_final: 0.7329 (p0) REVERT: A 243 TYR cc_start: 0.7090 (m-10) cc_final: 0.6880 (m-80) REVERT: A 399 MET cc_start: 0.7293 (tpt) cc_final: 0.7049 (tpp) REVERT: B 246 MET cc_start: 0.9126 (mmt) cc_final: 0.8489 (mmm) REVERT: B 440 HIS cc_start: 0.7598 (m-70) cc_final: 0.7300 (m-70) REVERT: C 395 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: D 119 ASN cc_start: 0.7487 (p0) cc_final: 0.7212 (p0) REVERT: E 73 ILE cc_start: 0.8951 (mm) cc_final: 0.8687 (mm) REVERT: F 119 ASN cc_start: 0.7575 (p0) cc_final: 0.7259 (p0) REVERT: F 246 MET cc_start: 0.9051 (mmt) cc_final: 0.8729 (mmt) REVERT: F 417 LYS cc_start: 0.7445 (mmmt) cc_final: 0.7200 (mmtt) REVERT: G 243 TYR cc_start: 0.7243 (m-10) cc_final: 0.7032 (m-80) REVERT: G 397 MET cc_start: 0.7299 (mmm) cc_final: 0.7013 (mmm) outliers start: 14 outliers final: 0 residues processed: 411 average time/residue: 0.3444 time to fit residues: 210.8428 Evaluate side-chains 249 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 203 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 122 GLN B 248 ASN B 287 ASN C 125 ASN C 248 ASN C 304 ASN D 248 ASN E 248 ASN F 248 ASN G 82 GLN G 248 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21476 Z= 0.158 Angle : 0.604 6.580 29029 Z= 0.291 Chirality : 0.042 0.171 3213 Planarity : 0.006 0.067 3640 Dihedral : 6.116 54.748 2929 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.83 % Allowed : 11.50 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2576 helix: -0.07 (0.16), residues: 1043 sheet: -2.64 (0.18), residues: 574 loop : -2.29 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 102 HIS 0.001 0.000 HIS D 141 PHE 0.025 0.001 PHE F 412 TYR 0.018 0.001 TYR D 259 ARG 0.006 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 292 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8601 (mm) cc_final: 0.8308 (mm) REVERT: A 243 TYR cc_start: 0.7013 (m-10) cc_final: 0.6774 (m-80) REVERT: A 399 MET cc_start: 0.7407 (tpt) cc_final: 0.7183 (tpp) REVERT: B 375 MET cc_start: 0.7737 (mmt) cc_final: 0.7494 (mmt) REVERT: B 440 HIS cc_start: 0.7639 (m-70) cc_final: 0.7364 (m-70) REVERT: D 230 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7760 (mp) REVERT: D 255 ARG cc_start: 0.8037 (mpt180) cc_final: 0.7468 (mpt180) REVERT: E 73 ILE cc_start: 0.8675 (mm) cc_final: 0.8456 (mm) REVERT: E 379 ARG cc_start: 0.6461 (mtt-85) cc_final: 0.6235 (mtm-85) REVERT: F 246 MET cc_start: 0.9016 (mmt) cc_final: 0.8590 (mmt) REVERT: G 397 MET cc_start: 0.7378 (mmm) cc_final: 0.7064 (mmm) outliers start: 64 outliers final: 41 residues processed: 340 average time/residue: 0.2921 time to fit residues: 158.6721 Evaluate side-chains 294 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 252 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 chunk 189 optimal weight: 4.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 123 HIS C 125 ASN C 304 ASN F 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21476 Z= 0.203 Angle : 0.597 6.070 29029 Z= 0.288 Chirality : 0.043 0.230 3213 Planarity : 0.005 0.055 3640 Dihedral : 5.744 46.029 2926 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.72 % Allowed : 13.27 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 2576 helix: 0.47 (0.17), residues: 1008 sheet: -2.47 (0.19), residues: 574 loop : -2.10 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 102 HIS 0.004 0.001 HIS B 123 PHE 0.014 0.001 PHE A 209 TYR 0.018 0.001 TYR E 259 ARG 0.007 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 263 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8580 (mm) cc_final: 0.8249 (mm) REVERT: A 82 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.5302 (mp-120) REVERT: A 243 TYR cc_start: 0.7050 (m-10) cc_final: 0.6792 (m-80) REVERT: A 399 MET cc_start: 0.7418 (tpt) cc_final: 0.7146 (tpp) REVERT: B 375 MET cc_start: 0.7788 (mmt) cc_final: 0.7456 (mmt) REVERT: B 440 HIS cc_start: 0.7701 (m-70) cc_final: 0.7455 (m-70) REVERT: D 230 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7771 (mp) REVERT: E 73 ILE cc_start: 0.8784 (mm) cc_final: 0.8550 (mm) REVERT: F 246 MET cc_start: 0.9002 (mmt) cc_final: 0.8528 (mmt) REVERT: G 160 MET cc_start: 0.7854 (mtm) cc_final: 0.7609 (mtt) REVERT: G 386 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7276 (m) outliers start: 84 outliers final: 61 residues processed: 327 average time/residue: 0.2761 time to fit residues: 146.6684 Evaluate side-chains 314 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 67 optimal weight: 0.0010 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN C 440 HIS F 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21476 Z= 0.185 Angle : 0.584 6.202 29029 Z= 0.279 Chirality : 0.042 0.174 3213 Planarity : 0.005 0.070 3640 Dihedral : 5.557 44.492 2926 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.58 % Allowed : 14.11 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2576 helix: 0.67 (0.17), residues: 1008 sheet: -2.28 (0.19), residues: 574 loop : -1.90 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 213 HIS 0.002 0.000 HIS C 106 PHE 0.011 0.001 PHE A 209 TYR 0.017 0.001 TYR B 259 ARG 0.003 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 269 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8586 (mm) cc_final: 0.8255 (mm) REVERT: A 243 TYR cc_start: 0.7013 (m-10) cc_final: 0.6773 (m-80) REVERT: B 375 MET cc_start: 0.7825 (mmt) cc_final: 0.7496 (mmt) REVERT: B 440 HIS cc_start: 0.7694 (m-70) cc_final: 0.7455 (m-70) REVERT: D 152 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7541 (mt) REVERT: E 73 ILE cc_start: 0.8775 (mm) cc_final: 0.8548 (mm) REVERT: E 152 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7557 (mt) REVERT: F 152 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7435 (mt) REVERT: F 246 MET cc_start: 0.8992 (mmt) cc_final: 0.8543 (mmt) REVERT: G 386 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7260 (m) outliers start: 81 outliers final: 62 residues processed: 324 average time/residue: 0.2715 time to fit residues: 143.1901 Evaluate side-chains 316 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 250 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.0020 chunk 224 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 304 ASN C 440 HIS D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 21476 Z= 0.469 Angle : 0.742 7.702 29029 Z= 0.362 Chirality : 0.049 0.197 3213 Planarity : 0.007 0.076 3640 Dihedral : 6.043 46.934 2926 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.20 % Allowed : 16.10 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.17), residues: 2576 helix: 0.49 (0.17), residues: 1001 sheet: -2.81 (0.19), residues: 602 loop : -2.11 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 142 HIS 0.004 0.001 HIS C 106 PHE 0.020 0.002 PHE A 209 TYR 0.030 0.002 TYR C 259 ARG 0.005 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 268 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8684 (mm) cc_final: 0.8303 (mm) REVERT: A 82 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.5571 (mp-120) REVERT: A 243 TYR cc_start: 0.7301 (m-10) cc_final: 0.7058 (m-80) REVERT: B 51 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.6158 (t80) REVERT: B 375 MET cc_start: 0.7950 (mmt) cc_final: 0.7603 (mmt) REVERT: B 440 HIS cc_start: 0.7738 (m-70) cc_final: 0.7501 (m-70) REVERT: C 375 MET cc_start: 0.7737 (mmm) cc_final: 0.7236 (mmt) REVERT: F 246 MET cc_start: 0.9049 (mmt) cc_final: 0.8585 (mmt) REVERT: G 362 MET cc_start: 0.7987 (mtt) cc_final: 0.7735 (mtt) REVERT: G 386 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7273 (m) outliers start: 95 outliers final: 76 residues processed: 333 average time/residue: 0.2766 time to fit residues: 149.3143 Evaluate side-chains 322 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 243 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 304 ASN C 440 HIS D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21476 Z= 0.182 Angle : 0.600 6.932 29029 Z= 0.288 Chirality : 0.041 0.162 3213 Planarity : 0.006 0.064 3640 Dihedral : 5.626 44.750 2926 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.89 % Allowed : 17.91 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2576 helix: 0.74 (0.17), residues: 1008 sheet: -2.52 (0.19), residues: 602 loop : -1.80 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 251 HIS 0.002 0.000 HIS C 106 PHE 0.010 0.001 PHE B 412 TYR 0.018 0.001 TYR C 259 ARG 0.007 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 265 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8577 (mm) cc_final: 0.8230 (mm) REVERT: B 51 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5938 (t80) REVERT: B 152 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7350 (mt) REVERT: B 375 MET cc_start: 0.8054 (mmt) cc_final: 0.7651 (mmt) REVERT: B 440 HIS cc_start: 0.7700 (m-70) cc_final: 0.7460 (m-70) REVERT: C 375 MET cc_start: 0.7698 (mmm) cc_final: 0.7213 (mmt) REVERT: C 396 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7814 (mmmt) REVERT: E 51 TYR cc_start: 0.6070 (OUTLIER) cc_final: 0.5574 (t80) REVERT: E 73 ILE cc_start: 0.8881 (mm) cc_final: 0.8672 (mm) REVERT: F 152 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7732 (mt) REVERT: F 246 MET cc_start: 0.9043 (mmt) cc_final: 0.8578 (mmt) REVERT: G 386 VAL cc_start: 0.7568 (OUTLIER) cc_final: 0.7294 (m) outliers start: 88 outliers final: 67 residues processed: 325 average time/residue: 0.2761 time to fit residues: 145.5340 Evaluate side-chains 324 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 252 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 0.0670 chunk 139 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 HIS C 304 ASN C 440 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21476 Z= 0.149 Angle : 0.571 7.925 29029 Z= 0.271 Chirality : 0.040 0.160 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.312 42.220 2926 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.54 % Allowed : 18.80 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2576 helix: 0.91 (0.17), residues: 1008 sheet: -2.14 (0.20), residues: 588 loop : -1.67 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 251 HIS 0.003 0.000 HIS A 141 PHE 0.016 0.001 PHE C 52 TYR 0.015 0.001 TYR B 259 ARG 0.005 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 266 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8571 (mm) cc_final: 0.8221 (mm) REVERT: A 125 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.6956 (m-40) REVERT: A 152 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7593 (mt) REVERT: B 51 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5905 (t80) REVERT: B 152 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7402 (mt) REVERT: B 375 MET cc_start: 0.8052 (mmt) cc_final: 0.7576 (mmt) REVERT: C 152 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7872 (mp) REVERT: C 375 MET cc_start: 0.7698 (mmm) cc_final: 0.7250 (mmt) REVERT: D 152 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7503 (mt) REVERT: E 51 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.5472 (t80) REVERT: E 73 ILE cc_start: 0.8839 (mm) cc_final: 0.8619 (mm) REVERT: E 152 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7554 (mt) REVERT: F 152 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7710 (mt) REVERT: F 246 MET cc_start: 0.9020 (mmt) cc_final: 0.8556 (mmt) REVERT: G 152 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7751 (mp) REVERT: G 160 MET cc_start: 0.7842 (mtm) cc_final: 0.7580 (mtt) REVERT: G 386 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7224 (m) outliers start: 80 outliers final: 53 residues processed: 324 average time/residue: 0.2845 time to fit residues: 149.0041 Evaluate side-chains 314 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21476 Z= 0.193 Angle : 0.595 9.662 29029 Z= 0.282 Chirality : 0.041 0.204 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.272 41.867 2926 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.45 % Allowed : 19.50 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2576 helix: 1.06 (0.17), residues: 1001 sheet: -1.99 (0.20), residues: 588 loop : -1.72 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 251 HIS 0.003 0.000 HIS E 141 PHE 0.010 0.001 PHE E 52 TYR 0.014 0.001 TYR B 259 ARG 0.006 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 253 time to evaluate : 2.800 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5679 (t80) REVERT: A 73 ILE cc_start: 0.8572 (mm) cc_final: 0.8226 (mm) REVERT: A 125 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: A 379 ARG cc_start: 0.7195 (mtm-85) cc_final: 0.6582 (mmt90) REVERT: B 51 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.5992 (t80) REVERT: B 152 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7395 (mt) REVERT: B 375 MET cc_start: 0.8067 (mmt) cc_final: 0.7569 (mmt) REVERT: C 152 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7805 (mp) REVERT: C 375 MET cc_start: 0.7631 (mmm) cc_final: 0.7280 (mmt) REVERT: D 152 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7590 (mt) REVERT: D 362 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7574 (mtp) REVERT: E 73 ILE cc_start: 0.8852 (mm) cc_final: 0.8635 (mm) REVERT: E 152 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7584 (mt) REVERT: F 152 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7721 (mt) REVERT: F 246 MET cc_start: 0.8993 (mmt) cc_final: 0.8510 (mmt) REVERT: G 152 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7637 (mt) REVERT: G 386 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7159 (m) outliers start: 78 outliers final: 56 residues processed: 304 average time/residue: 0.2672 time to fit residues: 134.9487 Evaluate side-chains 318 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 251 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN F 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21476 Z= 0.215 Angle : 0.603 9.907 29029 Z= 0.286 Chirality : 0.042 0.224 3213 Planarity : 0.005 0.061 3640 Dihedral : 5.288 41.917 2926 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.80 % Allowed : 19.02 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2576 helix: 1.10 (0.18), residues: 1001 sheet: -1.99 (0.20), residues: 602 loop : -1.74 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 213 HIS 0.003 0.001 HIS B 141 PHE 0.010 0.001 PHE A 52 TYR 0.015 0.001 TYR B 259 ARG 0.005 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 255 time to evaluate : 2.327 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.5692 (t80) REVERT: A 73 ILE cc_start: 0.8569 (mm) cc_final: 0.8218 (mm) REVERT: A 125 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7029 (m-40) REVERT: A 379 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6613 (mmt90) REVERT: B 51 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6016 (t80) REVERT: B 152 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7355 (mt) REVERT: B 375 MET cc_start: 0.8078 (mmt) cc_final: 0.7572 (mmt) REVERT: C 375 MET cc_start: 0.7617 (mmm) cc_final: 0.7289 (mmt) REVERT: D 152 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7639 (mt) REVERT: D 246 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8455 (mmm) REVERT: D 362 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7530 (mtp) REVERT: F 152 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7788 (mt) REVERT: F 246 MET cc_start: 0.8999 (mmt) cc_final: 0.8553 (mmt) REVERT: F 375 MET cc_start: 0.7833 (mmm) cc_final: 0.7217 (mmt) REVERT: G 152 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7574 (mp) REVERT: G 386 VAL cc_start: 0.7428 (OUTLIER) cc_final: 0.7147 (m) outliers start: 86 outliers final: 64 residues processed: 310 average time/residue: 0.2680 time to fit residues: 136.3799 Evaluate side-chains 326 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 252 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 116 optimal weight: 0.0570 chunk 171 optimal weight: 0.2980 chunk 258 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN F 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21476 Z= 0.153 Angle : 0.579 10.303 29029 Z= 0.274 Chirality : 0.040 0.202 3213 Planarity : 0.005 0.059 3640 Dihedral : 5.118 40.430 2926 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.10 % Allowed : 19.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2576 helix: 1.16 (0.17), residues: 1001 sheet: -1.66 (0.21), residues: 588 loop : -1.65 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 251 HIS 0.003 0.000 HIS G 141 PHE 0.009 0.001 PHE E 342 TYR 0.013 0.001 TYR E 120 ARG 0.005 0.000 ARG C 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 267 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8681 (mm) cc_final: 0.8297 (mm) REVERT: A 125 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.6960 (m-40) REVERT: A 152 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7683 (mt) REVERT: A 379 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6607 (mmt90) REVERT: B 51 TYR cc_start: 0.6745 (OUTLIER) cc_final: 0.6128 (t80) REVERT: B 152 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 375 MET cc_start: 0.8090 (mmt) cc_final: 0.7542 (mmt) REVERT: C 152 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7816 (mp) REVERT: C 375 MET cc_start: 0.7631 (mmm) cc_final: 0.7313 (mmt) REVERT: D 152 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7650 (mt) REVERT: D 399 MET cc_start: 0.7195 (tpt) cc_final: 0.6900 (tpp) REVERT: E 110 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8455 (p) REVERT: E 152 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7577 (mt) REVERT: F 152 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7739 (mt) REVERT: F 246 MET cc_start: 0.9012 (mmt) cc_final: 0.8589 (mmt) REVERT: F 375 MET cc_start: 0.7865 (mmm) cc_final: 0.7212 (mmt) REVERT: G 141 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7942 (m90) REVERT: G 160 MET cc_start: 0.7674 (mtm) cc_final: 0.7242 (mtt) REVERT: G 386 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7090 (m) outliers start: 70 outliers final: 53 residues processed: 313 average time/residue: 0.2710 time to fit residues: 138.7743 Evaluate side-chains 324 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 260 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 441 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.8980 chunk 218 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 189 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122461 restraints weight = 25806.351| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.97 r_work: 0.3213 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21476 Z= 0.146 Angle : 0.578 10.412 29029 Z= 0.272 Chirality : 0.040 0.198 3213 Planarity : 0.005 0.058 3640 Dihedral : 4.976 38.821 2926 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.79 % Allowed : 20.39 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2576 helix: 1.27 (0.17), residues: 1001 sheet: -1.39 (0.21), residues: 588 loop : -1.58 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 251 HIS 0.002 0.000 HIS B 141 PHE 0.019 0.001 PHE B 209 TYR 0.013 0.001 TYR E 120 ARG 0.005 0.000 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4910.71 seconds wall clock time: 89 minutes 4.25 seconds (5344.25 seconds total)