Starting phenix.real_space_refine on Mon Apr 15 01:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozi_17310/04_2024/8ozi_17310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozi_17310/04_2024/8ozi_17310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozi_17310/04_2024/8ozi_17310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozi_17310/04_2024/8ozi_17310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozi_17310/04_2024/8ozi_17310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozi_17310/04_2024/8ozi_17310_updated.pdb" } resolution = 3.22 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. 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 136 5.49 5 S 96 5.16 5 C 20278 2.51 5 N 5314 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 14": "OD1" <-> "OD2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 488": "OE1" <-> "OE2" Residue "E ASP 13": "OD1" <-> "OD2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 133": "OD1" <-> "OD2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F ASP 309": "OD1" <-> "OD2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 449": "OE1" <-> "OE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 119": "OD1" <-> "OD2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 244": "OE1" <-> "OE2" Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 301": "OE1" <-> "OE2" Residue "G GLU 306": "OE1" <-> "OE2" Residue "G ASP 316": "OD1" <-> "OD2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32092 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.65, per 1000 atoms: 0.52 Number of scatterers: 32092 At special positions: 0 Unit cell: (179.08, 208.12, 165.77, 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 96 16.00 P 136 15.00 O 6268 8.00 N 5314 7.00 C 20278 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: 13.39 Conformation dependent library (CDL) restraints added in 6.3 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 134 helices and 37 sheets defined 34.2% alpha, 13.0% beta 25 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 13.53 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.813A pdb=" N TRP A 46 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 49 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 220 through 223 removed outlier: 4.166A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.551A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 258 through 279 removed outlier: 4.112A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 354 through 367 removed outlier: 4.722A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 383 removed outlier: 4.093A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 23 through 30 Processing helix chain 'B' and resid 47 through 61 removed outlier: 3.836A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.600A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 removed outlier: 3.717A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.746A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 4.039A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.584A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.735A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 72 through 88 Processing helix chain 'C' and resid 110 through 113 No H-bonds generated for 'chain 'C' and resid 110 through 113' Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.550A pdb=" N LEU C 128 " --> pdb=" O TRP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 220 through 223 removed outlier: 4.466A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 223' Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.616A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 232' Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 258 through 279 removed outlier: 3.885A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 354 through 367 removed outlier: 4.994A pdb=" N ASN C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 383 removed outlier: 4.652A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 47 through 61 removed outlier: 3.605A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.605A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 131 removed outlier: 3.774A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 231 through 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' Processing helix chain 'D' and resid 249 through 263 Processing helix chain 'D' and resid 332 through 350 removed outlier: 4.154A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 376 removed outlier: 3.711A pdb=" N GLU D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.598A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 490 Processing helix chain 'D' and resid 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 43 through 55 removed outlier: 3.848A pdb=" N TRP E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 110 through 113 No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 124 through 137 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 228 through 232 removed outlier: 3.580A pdb=" N GLU E 231 " --> pdb=" O PRO E 228 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 232' Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 258 through 279 removed outlier: 3.667A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 354 through 367 removed outlier: 4.620A pdb=" N ASN E 367 " --> pdb=" O ARG E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 383 removed outlier: 3.721A pdb=" N THR E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 23 through 30 Processing helix chain 'F' and resid 47 through 61 removed outlier: 3.522A pdb=" N LYS F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 110 through 130 removed outlier: 3.689A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 150 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 206 through 213 Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'F' and resid 249 through 263 removed outlier: 3.664A pdb=" N ALA F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 350 removed outlier: 4.438A pdb=" N GLN F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 376 removed outlier: 3.694A pdb=" N GLU F 375 " --> pdb=" O ASP F 371 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 452 through 464 removed outlier: 3.549A pdb=" N LEU F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS F 464 " --> pdb=" O LEU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 490 removed outlier: 3.553A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'G' and resid 15 through 28 Processing helix chain 'G' and resid 35 through 38 No H-bonds generated for 'chain 'G' and resid 35 through 38' Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 72 through 88 Processing helix chain 'G' and resid 91 through 93 No H-bonds generated for 'chain 'G' and resid 91 through 93' Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 110 through 113 No H-bonds generated for 'chain 'G' and resid 110 through 113' Processing helix chain 'G' and resid 124 through 137 removed outlier: 3.634A pdb=" N LEU G 128 " --> pdb=" O TRP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.691A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 228 through 232' Processing helix chain 'G' and resid 235 through 237 No H-bonds generated for 'chain 'G' and resid 235 through 237' Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 258 through 279 removed outlier: 3.941A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 303 No H-bonds generated for 'chain 'G' and resid 301 through 303' Processing helix chain 'G' and resid 354 through 367 removed outlier: 4.912A pdb=" N ASN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 383 removed outlier: 4.106A pdb=" N THR G 375 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 23 through 30 Processing helix chain 'H' and resid 47 through 61 removed outlier: 3.672A pdb=" N LYS H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 81 No H-bonds generated for 'chain 'H' and resid 78 through 81' Processing helix chain 'H' and resid 98 through 105 removed outlier: 3.603A pdb=" N PHE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 130 removed outlier: 4.212A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 206 through 213 Processing helix chain 'H' and resid 231 through 233 No H-bonds generated for 'chain 'H' and resid 231 through 233' Processing helix chain 'H' and resid 249 through 264 Processing helix chain 'H' and resid 332 through 350 removed outlier: 3.536A pdb=" N TYR H 346 " --> pdb=" O SER H 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 376 Processing helix chain 'H' and resid 452 through 464 removed outlier: 3.579A pdb=" N LEU H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 490 removed outlier: 3.641A pdb=" N ASP H 484 " --> pdb=" O LEU H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 505 No H-bonds generated for 'chain 'H' and resid 503 through 505' Processing sheet with id= A, first strand: chain 'A' and resid 94 through 98 removed outlier: 8.279A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS A 4 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 8 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER A 64 " --> pdb=" O SER A 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= C, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= E, first strand: chain 'A' and resid 283 through 286 Processing sheet with id= F, first strand: chain 'A' and resid 390 through 394 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.074A pdb=" N VAL B 138 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE B 44 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 140 " --> pdb=" O ILE B 44 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 282 through 286 Processing sheet with id= I, first strand: chain 'B' and resid 356 through 361 removed outlier: 6.419A pdb=" N ASN B 382 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 359 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 384 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA B 361 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 386 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 94 through 98 removed outlier: 8.913A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 4 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N PHE C 60 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 6 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 62 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 8 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER C 64 " --> pdb=" O SER C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 169 through 172 Processing sheet with id= L, first strand: chain 'C' and resid 175 through 177 Processing sheet with id= M, first strand: chain 'C' and resid 186 through 188 Processing sheet with id= N, first strand: chain 'C' and resid 283 through 286 Processing sheet with id= O, first strand: chain 'C' and resid 390 through 394 Processing sheet with id= P, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.481A pdb=" N VAL D 138 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 44 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE D 140 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 282 through 286 removed outlier: 3.524A pdb=" N ALA D 300 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 356 through 361 removed outlier: 6.536A pdb=" N ASN D 382 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 359 " --> pdb=" O ASN D 382 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 384 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA D 361 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL D 386 " --> pdb=" O ALA D 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 417 through 420 Processing sheet with id= T, first strand: chain 'E' and resid 94 through 98 removed outlier: 8.407A pdb=" N ILE E 95 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE E 60 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU E 97 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU E 62 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS E 4 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE E 60 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE E 6 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU E 62 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER E 8 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER E 64 " --> pdb=" O SER E 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.508A pdb=" N TYR E 171 " --> pdb=" O PHE E 410 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.526A pdb=" N SER E 324 " --> pdb=" O SER E 338 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 186 through 188 removed outlier: 3.692A pdb=" N THR E 216 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS E 188 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 283 through 286 Processing sheet with id= Y, first strand: chain 'E' and resid 390 through 394 Processing sheet with id= Z, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.076A pdb=" N VAL F 138 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE F 44 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE F 140 " --> pdb=" O ILE F 44 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 282 through 286 Processing sheet with id= AB, first strand: chain 'F' and resid 356 through 361 removed outlier: 6.286A pdb=" N ASN F 382 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE F 359 " --> pdb=" O ASN F 382 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 384 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA F 361 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL F 386 " --> pdb=" O ALA F 361 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 117 through 119 removed outlier: 8.104A pdb=" N ILE G 118 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ILE G 95 " --> pdb=" O CYS G 58 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE G 60 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU G 97 " --> pdb=" O PHE G 60 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU G 62 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS G 4 " --> pdb=" O CYS G 58 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE G 60 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE G 6 " --> pdb=" O PHE G 60 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU G 62 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER G 8 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER G 64 " --> pdb=" O SER G 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 169 through 172 Processing sheet with id= AE, first strand: chain 'G' and resid 175 through 177 Processing sheet with id= AF, first strand: chain 'G' and resid 186 through 188 Processing sheet with id= AG, first strand: chain 'G' and resid 283 through 286 Processing sheet with id= AH, first strand: chain 'G' and resid 390 through 394 removed outlier: 3.840A pdb=" N VAL G 403 " --> pdb=" O PHE G 391 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 393 " --> pdb=" O VAL G 401 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 92 through 95 removed outlier: 6.562A pdb=" N VAL H 138 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE H 44 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE H 140 " --> pdb=" O ILE H 44 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 282 through 286 Processing sheet with id= AK, first strand: chain 'H' and resid 356 through 361 removed outlier: 6.363A pdb=" N ASN H 382 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE H 359 " --> pdb=" O ASN H 382 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL H 384 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA H 361 " --> pdb=" O VAL H 384 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL H 386 " --> pdb=" O ALA H 361 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR H 387 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE H 445 " --> pdb=" O THR H 387 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER H 389 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE H 443 " --> pdb=" O SER H 389 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 14.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4931 1.31 - 1.43: 9816 1.43 - 1.56: 17993 1.56 - 1.69: 272 1.69 - 1.81: 148 Bond restraints: 33160 Sorted by residual: bond pdb=" C2B NAD C 501 " pdb=" C3B NAD C 501 " ideal model delta sigma weight residual 1.524 1.258 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C2B NAD G 501 " pdb=" C3B NAD G 501 " ideal model delta sigma weight residual 1.524 1.265 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C4D NAD C 501 " pdb=" O4D NAD C 501 " ideal model delta sigma weight residual 1.445 1.291 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C4D NAD G 501 " pdb=" O4D NAD G 501 " ideal model delta sigma weight residual 1.445 1.292 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C4B NAD G 501 " pdb=" C5B NAD G 501 " ideal model delta sigma weight residual 1.522 1.375 0.147 2.00e-02 2.50e+03 5.39e+01 ... (remaining 33155 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.22: 1031 105.22 - 112.57: 17277 112.57 - 119.92: 11895 119.92 - 127.27: 14655 127.27 - 134.62: 544 Bond angle restraints: 45402 Sorted by residual: angle pdb=" C GLU F 352 " pdb=" N TYR F 353 " pdb=" CA TYR F 353 " ideal model delta sigma weight residual 120.60 131.06 -10.46 1.53e+00 4.27e-01 4.67e+01 angle pdb=" C4D NAD C 501 " pdb=" C3D NAD C 501 " pdb=" O3D NAD C 501 " ideal model delta sigma weight residual 108.31 127.82 -19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" C4D NAD G 501 " pdb=" C3D NAD G 501 " pdb=" O3D NAD G 501 " ideal model delta sigma weight residual 108.31 127.48 -19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" C1D NAD G 501 " pdb=" C2D NAD G 501 " pdb=" O2D NAD G 501 " ideal model delta sigma weight residual 110.62 128.49 -17.87 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C1D NAD C 501 " pdb=" C2D NAD C 501 " pdb=" O2D NAD C 501 " ideal model delta sigma weight residual 110.62 128.42 -17.80 3.00e+00 1.11e-01 3.52e+01 ... (remaining 45397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 19183 33.80 - 67.60: 793 67.60 - 101.40: 54 101.40 - 135.20: 5 135.20 - 169.00: 15 Dihedral angle restraints: 20050 sinusoidal: 9542 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 7 " pdb=" C1' U N 7 " pdb=" N1 U N 7 " pdb=" C2 U N 7 " ideal model delta sinusoidal sigma weight residual 200.00 31.00 169.00 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U M 13 " pdb=" C1' U M 13 " pdb=" N1 U M 13 " pdb=" C2 U M 13 " ideal model delta sinusoidal sigma weight residual 200.00 36.83 163.17 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U K 13 " pdb=" C1' U K 13 " pdb=" N1 U K 13 " pdb=" C2 U K 13 " ideal model delta sinusoidal sigma weight residual 200.00 39.38 160.62 1 1.50e+01 4.44e-03 8.29e+01 ... (remaining 20047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.945: 4974 0.945 - 1.890: 0 1.890 - 2.835: 8 2.835 - 3.780: 0 3.780 - 4.726: 2 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1B NAD C 501 " pdb=" C2B NAD C 501 " pdb=" N9A NAD C 501 " pdb=" O4B NAD C 501 " both_signs ideal model delta sigma weight residual False 2.35 -2.38 4.73 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" C1B NAD G 501 " pdb=" C2B NAD G 501 " pdb=" N9A NAD G 501 " pdb=" O4B NAD G 501 " both_signs ideal model delta sigma weight residual False 2.35 -2.34 4.68 2.00e-01 2.50e+01 5.49e+02 chirality pdb=" C3D NAD G 501 " pdb=" C2D NAD G 501 " pdb=" C4D NAD G 501 " pdb=" O3D NAD G 501 " both_signs ideal model delta sigma weight residual False -2.73 -0.01 -2.72 2.00e-01 2.50e+01 1.85e+02 ... (remaining 4981 not shown) Planarity restraints: 5242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 72 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO H 73 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 73 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 73 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 318 " -0.043 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO D 319 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 392 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO H 393 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 393 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 393 " 0.035 5.00e-02 4.00e+02 ... (remaining 5239 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 885 2.68 - 3.23: 30853 3.23 - 3.79: 51706 3.79 - 4.34: 72413 4.34 - 4.90: 114678 Nonbonded interactions: 270535 Sorted by model distance: nonbonded pdb=" OG SER G 288 " pdb=" O2 U N 9 " model vdw 2.121 2.440 nonbonded pdb=" OG SER B 493 " pdb=" OD1 ASP B 495 " model vdw 2.124 2.440 nonbonded pdb=" OG SER C 288 " pdb=" O2 U K 9 " model vdw 2.147 2.440 nonbonded pdb=" O PRO H 500 " pdb=" OH TYR H 506 " model vdw 2.173 2.440 nonbonded pdb=" O LYS H 11 " pdb=" OG SER H 272 " model vdw 2.174 2.440 ... (remaining 270530 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 'C' and resid 1 through 418) selection = chain 'E' selection = (chain 'G' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 7.500 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 92.510 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.005 0.266 33160 Z= 0.322 Angle : 0.771 19.512 45402 Z= 0.418 Chirality : 0.145 4.726 4984 Planarity : 0.005 0.070 5242 Dihedral : 17.635 168.998 13258 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.84 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.91 (0.14), residues: 3532 helix: 0.39 (0.15), residues: 1186 sheet: -1.04 (0.21), residues: 634 loop : -1.08 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 370 HIS 0.006 0.001 HIS C 160 PHE 0.026 0.002 PHE A 332 TYR 0.018 0.001 TYR G 285 ARG 0.007 0.001 ARG F 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4158 (mtt) cc_final: 0.3457 (mmm) REVERT: B 122 ILE cc_start: 0.9008 (tt) cc_final: 0.8786 (tt) REVERT: B 148 TYR cc_start: 0.6610 (t80) cc_final: 0.5930 (t80) REVERT: C 295 LEU cc_start: 0.7648 (pt) cc_final: 0.7407 (tp) REVERT: D 74 MET cc_start: 0.7989 (ppp) cc_final: 0.7176 (ppp) REVERT: E 3 ASN cc_start: 0.7999 (p0) cc_final: 0.7739 (p0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.4073 time to fit residues: 249.0964 Evaluate side-chains 250 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.0870 chunk 282 optimal weight: 0.0670 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN A 226 HIS A 358 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN C 69 ASN C 70 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN F 367 HIS H 251 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33160 Z= 0.161 Angle : 0.571 9.425 45402 Z= 0.299 Chirality : 0.042 0.267 4984 Planarity : 0.005 0.062 5242 Dihedral : 18.431 179.781 5970 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer: Outliers : 0.94 % Allowed : 6.95 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.72 (0.14), residues: 3532 helix: 0.68 (0.15), residues: 1192 sheet: -0.80 (0.21), residues: 608 loop : -1.14 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 219 HIS 0.007 0.001 HIS A 160 PHE 0.022 0.001 PHE A 343 TYR 0.017 0.001 TYR G 293 ARG 0.005 0.000 ARG F 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 303 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4274 (mtt) cc_final: 0.3580 (mmm) REVERT: B 122 ILE cc_start: 0.8906 (tt) cc_final: 0.8643 (tt) REVERT: B 148 TYR cc_start: 0.6517 (t80) cc_final: 0.6041 (t80) REVERT: B 324 LYS cc_start: 0.7437 (tmtt) cc_final: 0.6708 (mtmm) REVERT: C 162 LYS cc_start: 0.4063 (mmpt) cc_final: 0.3794 (mmpt) REVERT: D 430 GLN cc_start: 0.8474 (tp40) cc_final: 0.8125 (mm-40) REVERT: E 3 ASN cc_start: 0.8002 (p0) cc_final: 0.7732 (p0) REVERT: E 257 ARG cc_start: 0.5847 (mmm-85) cc_final: 0.5500 (mmm-85) REVERT: G 395 MET cc_start: 0.6806 (mmt) cc_final: 0.6565 (mmt) REVERT: H 435 MET cc_start: 0.4938 (mmt) cc_final: 0.4663 (mmt) outliers start: 30 outliers final: 23 residues processed: 320 average time/residue: 0.4370 time to fit residues: 232.4606 Evaluate side-chains 280 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 272 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 327 optimal weight: 0.9980 chunk 353 optimal weight: 0.7980 chunk 291 optimal weight: 0.5980 chunk 324 optimal weight: 0.0670 chunk 111 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 59 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN H 430 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 33160 Z= 0.153 Angle : 0.527 8.719 45402 Z= 0.277 Chirality : 0.041 0.191 4984 Planarity : 0.004 0.057 5242 Dihedral : 18.360 178.725 5970 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.78 % Favored : 94.85 % Rotamer: Outliers : 1.16 % Allowed : 9.36 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.59 (0.14), residues: 3532 helix: 0.78 (0.15), residues: 1204 sheet: -0.59 (0.21), residues: 614 loop : -1.14 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 219 HIS 0.026 0.001 HIS F 367 PHE 0.017 0.001 PHE F 224 TYR 0.018 0.001 TYR B 150 ARG 0.003 0.000 ARG H 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 295 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4273 (mtt) cc_final: 0.3545 (mmm) REVERT: A 336 MET cc_start: 0.5990 (mtm) cc_final: 0.5603 (ptt) REVERT: B 1 MET cc_start: 0.5398 (mmp) cc_final: 0.5051 (mmp) REVERT: B 122 ILE cc_start: 0.8901 (tt) cc_final: 0.8640 (tt) REVERT: B 148 TYR cc_start: 0.6086 (t80) cc_final: 0.5859 (t80) REVERT: B 324 LYS cc_start: 0.7309 (tmtt) cc_final: 0.6845 (mttp) REVERT: B 435 MET cc_start: 0.5721 (mmm) cc_final: 0.5468 (mmt) REVERT: C 126 ARG cc_start: 0.6163 (mmp-170) cc_final: 0.5793 (tpp80) REVERT: C 162 LYS cc_start: 0.3999 (mmpt) cc_final: 0.3743 (mmpt) REVERT: C 371 ASN cc_start: 0.7814 (m-40) cc_final: 0.7416 (t0) REVERT: E 3 ASN cc_start: 0.7920 (p0) cc_final: 0.7716 (p0) REVERT: E 278 LYS cc_start: 0.7952 (mttp) cc_final: 0.7598 (mmmt) REVERT: F 18 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7327 (mm-40) REVERT: H 248 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7426 (mp) outliers start: 37 outliers final: 28 residues processed: 315 average time/residue: 0.4883 time to fit residues: 258.7147 Evaluate side-chains 276 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 248 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.9990 chunk 246 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 328 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 ASN H 329 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33160 Z= 0.255 Angle : 0.572 9.976 45402 Z= 0.298 Chirality : 0.042 0.199 4984 Planarity : 0.005 0.059 5242 Dihedral : 18.392 179.770 5970 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.12 % Favored : 94.45 % Rotamer: Outliers : 2.16 % Allowed : 10.36 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.60 (0.14), residues: 3532 helix: 0.83 (0.15), residues: 1206 sheet: -0.68 (0.21), residues: 612 loop : -1.16 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 219 HIS 0.012 0.001 HIS F 367 PHE 0.040 0.002 PHE A 45 TYR 0.022 0.001 TYR A 251 ARG 0.005 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 258 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4242 (mtt) cc_final: 0.3524 (mmm) REVERT: A 277 MET cc_start: 0.7160 (mmm) cc_final: 0.6770 (mmm) REVERT: B 1 MET cc_start: 0.5037 (mmp) cc_final: 0.4771 (mmp) REVERT: B 122 ILE cc_start: 0.9052 (tt) cc_final: 0.8816 (tt) REVERT: B 148 TYR cc_start: 0.6057 (t80) cc_final: 0.5831 (t80) REVERT: B 324 LYS cc_start: 0.7475 (tmtt) cc_final: 0.6761 (mtmm) REVERT: C 371 ASN cc_start: 0.7881 (m-40) cc_final: 0.7447 (t0) REVERT: D 150 TYR cc_start: 0.7656 (m-80) cc_final: 0.7276 (m-80) REVERT: E 3 ASN cc_start: 0.8071 (p0) cc_final: 0.7842 (p0) REVERT: F 30 PHE cc_start: 0.7941 (m-80) cc_final: 0.7635 (m-80) REVERT: F 79 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: F 325 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7944 (t0) REVERT: G 158 PHE cc_start: 0.6236 (t80) cc_final: 0.5630 (t80) REVERT: G 342 PHE cc_start: 0.5845 (m-10) cc_final: 0.5564 (m-10) REVERT: H 248 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7509 (mp) outliers start: 69 outliers final: 46 residues processed: 304 average time/residue: 0.4123 time to fit residues: 211.7531 Evaluate side-chains 280 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 387 THR Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 5 optimal weight: 0.0270 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN C 226 HIS ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN G 102 GLN G 174 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33160 Z= 0.206 Angle : 0.538 9.112 45402 Z= 0.282 Chirality : 0.041 0.215 4984 Planarity : 0.004 0.060 5242 Dihedral : 18.322 179.501 5970 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.12 % Favored : 94.54 % Rotamer: Outliers : 1.81 % Allowed : 11.58 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.57 (0.14), residues: 3532 helix: 0.92 (0.15), residues: 1208 sheet: -0.65 (0.22), residues: 610 loop : -1.20 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 219 HIS 0.005 0.001 HIS G 320 PHE 0.032 0.001 PHE A 45 TYR 0.017 0.001 TYR H 411 ARG 0.003 0.000 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4222 (mtt) cc_final: 0.3520 (mmm) REVERT: B 1 MET cc_start: 0.5091 (mmp) cc_final: 0.4845 (mmp) REVERT: B 66 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7217 (p0) REVERT: B 122 ILE cc_start: 0.9040 (tt) cc_final: 0.8800 (tt) REVERT: B 324 LYS cc_start: 0.7514 (tmtt) cc_final: 0.6913 (mttp) REVERT: C 371 ASN cc_start: 0.7613 (m-40) cc_final: 0.7384 (t0) REVERT: D 147 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7212 (tp) REVERT: D 150 TYR cc_start: 0.7722 (m-80) cc_final: 0.7410 (m-80) REVERT: E 3 ASN cc_start: 0.8124 (p0) cc_final: 0.7823 (p0) REVERT: F 30 PHE cc_start: 0.7775 (m-80) cc_final: 0.7497 (m-80) REVERT: F 79 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: F 325 ASN cc_start: 0.8254 (m-40) cc_final: 0.7968 (t0) REVERT: G 158 PHE cc_start: 0.6333 (t80) cc_final: 0.5761 (t80) REVERT: G 373 TRP cc_start: 0.7998 (m100) cc_final: 0.7578 (m100) outliers start: 58 outliers final: 42 residues processed: 296 average time/residue: 0.4137 time to fit residues: 205.9843 Evaluate side-chains 282 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 237 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 226 HIS ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 302 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN H 360 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33160 Z= 0.338 Angle : 0.619 10.610 45402 Z= 0.321 Chirality : 0.043 0.223 4984 Planarity : 0.005 0.067 5242 Dihedral : 18.457 179.801 5970 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.86 % Favored : 93.86 % Rotamer: Outliers : 2.38 % Allowed : 12.27 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.76 (0.14), residues: 3532 helix: 0.77 (0.15), residues: 1208 sheet: -1.00 (0.21), residues: 626 loop : -1.22 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 219 HIS 0.005 0.001 HIS D 251 PHE 0.029 0.002 PHE A 45 TYR 0.018 0.002 TYR B 280 ARG 0.006 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 251 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4256 (mtt) cc_final: 0.3544 (mmm) REVERT: A 307 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7265 (mmtt) REVERT: B 1 MET cc_start: 0.4940 (mmp) cc_final: 0.4674 (mmp) REVERT: B 122 ILE cc_start: 0.9164 (tt) cc_final: 0.8947 (tt) REVERT: C 349 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6186 (tppt) REVERT: D 150 TYR cc_start: 0.7850 (m-80) cc_final: 0.7612 (m-80) REVERT: E 3 ASN cc_start: 0.8173 (p0) cc_final: 0.7849 (p0) REVERT: E 136 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: F 79 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: F 435 MET cc_start: 0.6375 (mmt) cc_final: 0.6162 (mmm) REVERT: G 158 PHE cc_start: 0.6577 (t80) cc_final: 0.6227 (t80) REVERT: G 299 LYS cc_start: 0.5476 (tttt) cc_final: 0.4956 (tttm) outliers start: 76 outliers final: 55 residues processed: 306 average time/residue: 0.4121 time to fit residues: 210.7298 Evaluate side-chains 284 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 387 THR Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33160 Z= 0.299 Angle : 0.594 9.949 45402 Z= 0.310 Chirality : 0.043 0.224 4984 Planarity : 0.005 0.072 5242 Dihedral : 18.428 179.750 5970 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.55 % Favored : 94.22 % Rotamer: Outliers : 2.60 % Allowed : 13.20 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.79 (0.14), residues: 3532 helix: 0.73 (0.15), residues: 1216 sheet: -0.84 (0.22), residues: 598 loop : -1.31 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 219 HIS 0.008 0.001 HIS A 160 PHE 0.035 0.002 PHE G 343 TYR 0.024 0.002 TYR A 293 ARG 0.005 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 246 time to evaluate : 3.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4258 (mtt) cc_final: 0.3552 (mmm) REVERT: A 307 LYS cc_start: 0.7752 (tmtt) cc_final: 0.7320 (mmtt) REVERT: B 1 MET cc_start: 0.4896 (mmp) cc_final: 0.4619 (mmp) REVERT: B 122 ILE cc_start: 0.9179 (tt) cc_final: 0.8971 (tt) REVERT: C 283 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 349 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6355 (tppt) REVERT: D 117 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8604 (mm) REVERT: E 3 ASN cc_start: 0.8148 (p0) cc_final: 0.7832 (p0) REVERT: E 136 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: E 395 MET cc_start: 0.6149 (mmm) cc_final: 0.5736 (mmm) REVERT: F 79 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: G 158 PHE cc_start: 0.6588 (t80) cc_final: 0.6311 (t80) REVERT: G 285 TYR cc_start: 0.6981 (t80) cc_final: 0.6637 (t80) REVERT: G 299 LYS cc_start: 0.5578 (tttt) cc_final: 0.4927 (tttm) REVERT: G 373 TRP cc_start: 0.7979 (m100) cc_final: 0.7690 (m100) outliers start: 83 outliers final: 63 residues processed: 307 average time/residue: 0.4178 time to fit residues: 216.6427 Evaluate side-chains 302 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 234 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 470 CYS Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 387 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33160 Z= 0.221 Angle : 0.559 10.843 45402 Z= 0.292 Chirality : 0.041 0.219 4984 Planarity : 0.004 0.073 5242 Dihedral : 18.360 179.889 5970 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.69 % Favored : 94.14 % Rotamer: Outliers : 2.28 % Allowed : 14.24 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.68 (0.14), residues: 3532 helix: 0.85 (0.15), residues: 1216 sheet: -0.81 (0.22), residues: 598 loop : -1.26 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 219 HIS 0.007 0.001 HIS A 160 PHE 0.024 0.001 PHE A 45 TYR 0.022 0.001 TYR A 293 ARG 0.006 0.000 ARG F 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 248 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4258 (mtt) cc_final: 0.3592 (mmm) REVERT: A 307 LYS cc_start: 0.7909 (tmtt) cc_final: 0.7444 (mmtt) REVERT: B 1 MET cc_start: 0.4729 (mmp) cc_final: 0.4445 (mmp) REVERT: B 122 ILE cc_start: 0.9130 (tt) cc_final: 0.8912 (tt) REVERT: B 148 TYR cc_start: 0.6050 (t80) cc_final: 0.5773 (t80) REVERT: C 283 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: C 349 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6429 (tppt) REVERT: D 117 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8648 (mm) REVERT: D 147 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7156 (tp) REVERT: D 430 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8049 (mm-40) REVERT: E 3 ASN cc_start: 0.8132 (p0) cc_final: 0.7821 (p0) REVERT: E 136 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: E 157 ILE cc_start: 0.8883 (mm) cc_final: 0.8664 (mm) REVERT: F 79 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: G 158 PHE cc_start: 0.6571 (t80) cc_final: 0.6267 (t80) outliers start: 73 outliers final: 63 residues processed: 301 average time/residue: 0.4234 time to fit residues: 213.5254 Evaluate side-chains 303 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 233 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 470 CYS Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 387 THR Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 6.9990 chunk 332 optimal weight: 0.0870 chunk 303 optimal weight: 8.9990 chunk 323 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 292 optimal weight: 0.4980 chunk 305 optimal weight: 5.9990 chunk 322 optimal weight: 0.0570 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33160 Z= 0.148 Angle : 0.529 11.008 45402 Z= 0.277 Chirality : 0.040 0.212 4984 Planarity : 0.004 0.069 5242 Dihedral : 18.243 178.845 5970 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 1.75 % Allowed : 14.89 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.53 (0.14), residues: 3532 helix: 1.03 (0.15), residues: 1208 sheet: -0.69 (0.21), residues: 630 loop : -1.23 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 219 HIS 0.006 0.001 HIS A 160 PHE 0.023 0.001 PHE A 45 TYR 0.019 0.001 TYR G 293 ARG 0.004 0.000 ARG F 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7389 (tp30) cc_final: 0.6727 (tt0) REVERT: A 193 MET cc_start: 0.4419 (mtt) cc_final: 0.3763 (mmm) REVERT: A 307 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7407 (mmtt) REVERT: B 1 MET cc_start: 0.4656 (mmp) cc_final: 0.4384 (mmp) REVERT: B 122 ILE cc_start: 0.9014 (tt) cc_final: 0.8790 (tt) REVERT: B 148 TYR cc_start: 0.6048 (t80) cc_final: 0.5765 (t80) REVERT: B 324 LYS cc_start: 0.7513 (tmtt) cc_final: 0.6872 (mttp) REVERT: C 283 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: D 117 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (mm) REVERT: D 147 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7269 (tp) REVERT: D 430 GLN cc_start: 0.8522 (tp40) cc_final: 0.8117 (mm-40) REVERT: E 3 ASN cc_start: 0.8010 (p0) cc_final: 0.7737 (p0) REVERT: E 157 ILE cc_start: 0.8781 (mm) cc_final: 0.8573 (mm) REVERT: E 395 MET cc_start: 0.5896 (mmm) cc_final: 0.5426 (mmm) REVERT: F 79 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: F 435 MET cc_start: 0.6340 (mmt) cc_final: 0.6131 (mmt) REVERT: G 158 PHE cc_start: 0.6531 (t80) cc_final: 0.6130 (t80) REVERT: G 285 TYR cc_start: 0.6809 (t80) cc_final: 0.6502 (t80) outliers start: 56 outliers final: 44 residues processed: 301 average time/residue: 0.4296 time to fit residues: 216.5037 Evaluate side-chains 295 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 302 GLN Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 9.9990 chunk 341 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33160 Z= 0.320 Angle : 0.614 10.834 45402 Z= 0.318 Chirality : 0.043 0.269 4984 Planarity : 0.005 0.075 5242 Dihedral : 18.383 179.532 5970 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 1.81 % Allowed : 15.05 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.70 (0.14), residues: 3532 helix: 0.85 (0.15), residues: 1216 sheet: -0.83 (0.22), residues: 588 loop : -1.28 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 219 HIS 0.008 0.001 HIS A 160 PHE 0.026 0.002 PHE A 332 TYR 0.021 0.002 TYR A 293 ARG 0.007 0.001 ARG F 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 249 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7481 (tp30) cc_final: 0.6694 (tt0) REVERT: A 193 MET cc_start: 0.4308 (mtt) cc_final: 0.3633 (mmm) REVERT: A 307 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7479 (mmtt) REVERT: B 1 MET cc_start: 0.4646 (mmp) cc_final: 0.4376 (mmp) REVERT: B 122 ILE cc_start: 0.9173 (tt) cc_final: 0.8962 (tt) REVERT: C 283 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: D 117 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 147 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7321 (tp) REVERT: D 430 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: E 3 ASN cc_start: 0.8170 (p0) cc_final: 0.7861 (p0) REVERT: E 136 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: E 157 ILE cc_start: 0.8879 (mm) cc_final: 0.8667 (mm) REVERT: E 395 MET cc_start: 0.5972 (mmm) cc_final: 0.5283 (mmm) REVERT: F 79 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: F 435 MET cc_start: 0.6409 (mmt) cc_final: 0.6209 (mmt) REVERT: G 158 PHE cc_start: 0.6753 (t80) cc_final: 0.6444 (t80) REVERT: G 285 TYR cc_start: 0.6863 (t80) cc_final: 0.6511 (t80) outliers start: 58 outliers final: 47 residues processed: 291 average time/residue: 0.4164 time to fit residues: 202.8154 Evaluate side-chains 288 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 235 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 422 THR Chi-restraints excluded: chain F residue 434 SER Chi-restraints excluded: chain G residue 223 PHE Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain H residue 66 ASN Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 387 THR Chi-restraints excluded: chain H residue 437 VAL Chi-restraints excluded: chain H residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.135072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105169 restraints weight = 66032.181| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.69 r_work: 0.3452 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33160 Z= 0.222 Angle : 0.561 9.280 45402 Z= 0.291 Chirality : 0.041 0.235 4984 Planarity : 0.004 0.075 5242 Dihedral : 18.315 179.118 5970 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % Rotamer: Outliers : 1.75 % Allowed : 15.33 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.64 (0.14), residues: 3532 helix: 0.91 (0.15), residues: 1216 sheet: -0.82 (0.21), residues: 624 loop : -1.24 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 219 HIS 0.007 0.001 HIS A 160 PHE 0.023 0.001 PHE B 358 TYR 0.020 0.001 TYR E 190 ARG 0.006 0.000 ARG F 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6524.46 seconds wall clock time: 121 minutes 9.57 seconds (7269.57 seconds total)