Starting phenix.real_space_refine (version: dev) on Sat May 14 19:44:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/05_2022/6sh3_10192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/05_2022/6sh3_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_10192/05_2022/6sh3_10192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/05_2022/6sh3_10192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/05_2022/6sh3_10192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sh3_10192/05_2022/6sh3_10192_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Convert atoms to be neutral 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 13.56, per 1000 atoms: 0.65 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: 10.09 Conformation dependent library (CDL) restraints added in 4.0 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: 2.03 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: 8.09 Time building geometry restraints manager: 10.82 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 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. 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: 0.640 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: 5.600 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.160 Process input model: 60.200 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 % 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 *********************** 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 : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 0 residues processed: 411 average time/residue: 0.3541 time to fit residues: 219.8714 Evaluate side-chains 244 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 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: 1.9990 chunk 151 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21476 Z= 0.166 Angle : 0.611 7.460 29029 Z= 0.296 Chirality : 0.042 0.171 3213 Planarity : 0.006 0.061 3640 Dihedral : 6.110 57.055 2926 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 2.74 % 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: -2.33 (0.16), residues: 2576 helix: -0.08 (0.16), residues: 1043 sheet: -2.47 (0.18), residues: 651 loop : -2.39 (0.20), residues: 882 *********************** 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 350 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 288 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 41 residues processed: 334 average time/residue: 0.2968 time to fit residues: 158.6147 Evaluate side-chains 288 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1913 time to fit residues: 18.1859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 195 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 21476 Z= 0.419 Angle : 0.730 7.038 29029 Z= 0.357 Chirality : 0.049 0.222 3213 Planarity : 0.007 0.080 3640 Dihedral : 6.198 47.730 2926 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 2.61 % 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: -2.38 (0.16), residues: 2576 helix: 0.11 (0.17), residues: 1022 sheet: -3.07 (0.18), residues: 602 loop : -2.27 (0.19), residues: 952 *********************** 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 330 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 317 average time/residue: 0.2797 time to fit residues: 144.0394 Evaluate side-chains 288 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1889 time to fit residues: 17.6160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8005 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21476 Z= 0.177 Angle : 0.602 8.870 29029 Z= 0.290 Chirality : 0.042 0.178 3213 Planarity : 0.005 0.059 3640 Dihedral : 5.765 44.768 2926 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.42 % 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: -1.81 (0.17), residues: 2576 helix: 0.55 (0.17), residues: 1008 sheet: -2.70 (0.19), residues: 588 loop : -1.96 (0.19), residues: 980 *********************** 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 298 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 2.637 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 283 average time/residue: 0.2873 time to fit residues: 130.9289 Evaluate side-chains 267 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 241 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1842 time to fit residues: 12.3822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.0000 chunk 224 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 21476 Z= 0.263 Angle : 0.624 7.376 29029 Z= 0.301 Chirality : 0.043 0.168 3213 Planarity : 0.006 0.085 3640 Dihedral : 5.681 44.450 2926 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.86 % 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: -1.69 (0.17), residues: 2576 helix: 0.68 (0.17), residues: 1008 sheet: -2.66 (0.19), residues: 602 loop : -1.90 (0.19), residues: 966 *********************** 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 304 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 2.533 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 17 residues processed: 294 average time/residue: 0.2767 time to fit residues: 132.3927 Evaluate side-chains 261 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1906 time to fit residues: 9.5917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 208 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.8034 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 21476 Z= 0.243 Angle : 0.615 8.087 29029 Z= 0.296 Chirality : 0.043 0.166 3213 Planarity : 0.006 0.065 3640 Dihedral : 5.611 44.199 2926 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 1.86 % 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: 0.80 (0.17), residues: 1001 sheet: -2.51 (0.19), residues: 602 loop : -1.89 (0.19), residues: 973 *********************** 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 304 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 3.027 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 286 average time/residue: 0.2836 time to fit residues: 132.1122 Evaluate side-chains 271 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1915 time to fit residues: 12.0331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 21476 Z= 0.365 Angle : 0.690 10.070 29029 Z= 0.334 Chirality : 0.046 0.179 3213 Planarity : 0.006 0.069 3640 Dihedral : 5.822 45.212 2926 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 1.99 % 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: -1.66 (0.17), residues: 2576 helix: 0.73 (0.18), residues: 1001 sheet: -2.58 (0.19), residues: 602 loop : -1.95 (0.19), residues: 973 *********************** 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 301 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 29 residues processed: 286 average time/residue: 0.2841 time to fit residues: 131.8635 Evaluate side-chains 274 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 2.567 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1850 time to fit residues: 13.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 170 optimal weight: 0.0030 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 21476 Z= 0.162 Angle : 0.596 9.551 29029 Z= 0.287 Chirality : 0.041 0.169 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.476 43.244 2926 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.80 % 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: -1.31 (0.17), residues: 2576 helix: 0.89 (0.17), residues: 1001 sheet: -2.23 (0.20), residues: 588 loop : -1.74 (0.19), residues: 987 *********************** 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 283 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 265 time to evaluate : 2.579 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 278 average time/residue: 0.2918 time to fit residues: 129.7132 Evaluate side-chains 254 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 243 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2126 time to fit residues: 7.8298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 210 optimal weight: 0.0980 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 G 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21476 Z= 0.176 Angle : 0.599 9.547 29029 Z= 0.287 Chirality : 0.041 0.162 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.341 42.066 2926 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.75 % 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: -1.17 (0.17), residues: 2576 helix: 0.99 (0.17), residues: 1001 sheet: -2.06 (0.20), residues: 588 loop : -1.72 (0.19), residues: 987 *********************** 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 276 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 2.803 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 271 average time/residue: 0.2849 time to fit residues: 126.0039 Evaluate side-chains 258 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 249 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1866 time to fit residues: 6.7547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21476 Z= 0.186 Angle : 0.610 10.545 29029 Z= 0.290 Chirality : 0.042 0.266 3213 Planarity : 0.005 0.061 3640 Dihedral : 5.285 41.407 2926 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.18 % 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: -1.03 (0.17), residues: 2576 helix: 1.07 (0.17), residues: 1001 sheet: -1.88 (0.20), residues: 588 loop : -1.68 (0.19), residues: 987 ********************** 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 259 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 2.681 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 257 average time/residue: 0.2863 time to fit residues: 120.0360 Evaluate side-chains 250 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1852 time to fit residues: 4.2413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.4980 chunk 218 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN C 304 ASN C 440 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122807 restraints weight = 25964.834| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.18 r_work: 0.3413 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3360 rms_B_bonded: 2.20 restraints_weight: 0.1250 r_work: 0.3319 rms_B_bonded: 2.70 restraints_weight: 0.0625 r_work: 0.3257 rms_B_bonded: 3.62 restraints_weight: 0.0312 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 21476 Z= 0.176 Angle : 0.604 10.810 29029 Z= 0.287 Chirality : 0.041 0.235 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.190 40.615 2926 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.22 % 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: -0.88 (0.17), residues: 2576 helix: 1.15 (0.17), residues: 1001 sheet: -1.68 (0.21), residues: 588 loop : -1.62 (0.19), residues: 987 =============================================================================== Job complete usr+sys time: 4241.71 seconds wall clock time: 78 minutes 3.43 seconds (4683.43 seconds total)