Starting phenix.real_space_refine on Fri Mar 6 19:05:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8it1_35703/03_2026/8it1_35703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it1_35703/03_2026/8it1_35703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8it1_35703/03_2026/8it1_35703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it1_35703/03_2026/8it1_35703.map" model { file = "/net/cci-nas-00/data/ceres_data/8it1_35703/03_2026/8it1_35703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it1_35703/03_2026/8it1_35703.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 180 5.49 5 S 92 5.16 5 C 21204 2.51 5 N 5672 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33844 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "J" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "N" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "O" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "P" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "C" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "G" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "H" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Time building chain proxies: 7.80, per 1000 atoms: 0.23 Number of scatterers: 33844 At special positions: 0 Unit cell: (118.56, 179.92, 271.44, 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 92 16.00 P 180 15.00 O 6696 8.00 N 5672 7.00 C 21204 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 - 3.00 Amino acid : True - 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: 2.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6968 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 41 sheets defined 39.6% alpha, 12.8% beta 7 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 62 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.945A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.825A pdb=" N ARG A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.816A pdb=" N LEU A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.625A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.700A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 3.707A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.099A pdb=" N ILE B 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 3.538A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.331A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.010A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.645A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.921A pdb=" N ILE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 280 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.763A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 304' Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.598A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.590A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 449 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.896A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 205 through 214 removed outlier: 4.285A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 265 removed outlier: 3.569A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 326 Processing helix chain 'E' and resid 331 through 351 Processing helix chain 'E' and resid 367 through 375 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.667A pdb=" N ALA E 483 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS E 485 " --> pdb=" O ARG E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 4.399A pdb=" N TYR E 505 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 65 through 70 removed outlier: 4.181A pdb=" N LYS F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 88 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 190 through 194 removed outlier: 3.876A pdb=" N LEU F 194 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 219 through 223 removed outlier: 4.153A pdb=" N ASP F 222 " --> pdb=" O TRP F 219 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE F 223 " --> pdb=" O GLU F 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 219 through 223' Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 257 through 279 Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.807A pdb=" N ASP F 303 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS F 304 " --> pdb=" O GLU F 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 300 through 304' Processing helix chain 'F' and resid 353 through 366 removed outlier: 3.503A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS F 366 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'F' and resid 421 through 438 removed outlier: 3.563A pdb=" N GLU F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU F 438 " --> pdb=" O ASN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 448 removed outlier: 3.571A pdb=" N LEU F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 22 through 30 Processing helix chain 'I' and resid 46 through 62 removed outlier: 3.796A pdb=" N LYS I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 83 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.631A pdb=" N ILE I 101 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 132 Processing helix chain 'I' and resid 144 through 150 Processing helix chain 'I' and resid 205 through 214 removed outlier: 3.626A pdb=" N GLN I 209 " --> pdb=" O GLN I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 218 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 248 through 265 Processing helix chain 'I' and resid 331 through 351 Processing helix chain 'I' and resid 367 through 377 removed outlier: 3.549A pdb=" N GLU I 375 " --> pdb=" O ASN I 371 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL I 376 " --> pdb=" O ALA I 372 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR I 377 " --> pdb=" O PHE I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 463 Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.962A pdb=" N ALA I 483 " --> pdb=" O THR I 479 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 485 " --> pdb=" O ARG I 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 28 removed outlier: 3.717A pdb=" N THR J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 56 Processing helix chain 'J' and resid 66 through 71 removed outlier: 3.976A pdb=" N LYS J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 66 through 71' Processing helix chain 'J' and resid 71 through 88 removed outlier: 3.575A pdb=" N LEU J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 4.137A pdb=" N ARG J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 138 Processing helix chain 'J' and resid 146 through 157 removed outlier: 4.230A pdb=" N SER J 150 " --> pdb=" O ASP J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 194 removed outlier: 3.589A pdb=" N LEU J 194 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.513A pdb=" N THR J 202 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 233 removed outlier: 3.930A pdb=" N THR J 232 " --> pdb=" O LYS J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 249 Processing helix chain 'J' and resid 257 through 280 Processing helix chain 'J' and resid 300 through 304 removed outlier: 3.587A pdb=" N ASP J 303 " --> pdb=" O LEU J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 366 removed outlier: 3.772A pdb=" N GLN J 357 " --> pdb=" O SER J 353 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS J 366 " --> pdb=" O ARG J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 385 Processing helix chain 'J' and resid 421 through 438 removed outlier: 3.550A pdb=" N GLU J 425 " --> pdb=" O GLU J 421 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU J 438 " --> pdb=" O ASN J 434 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 448 Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 22 through 30 Processing helix chain 'M' and resid 46 through 62 removed outlier: 3.515A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 Processing helix chain 'M' and resid 97 through 105 removed outlier: 3.585A pdb=" N ILE M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 132 Processing helix chain 'M' and resid 144 through 150 Processing helix chain 'M' and resid 205 through 214 removed outlier: 3.704A pdb=" N GLN M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 230 Processing helix chain 'M' and resid 248 through 265 removed outlier: 3.728A pdb=" N GLY M 265 " --> pdb=" O TYR M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 351 Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.831A pdb=" N TRP M 370 " --> pdb=" O ASN M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 463 Processing helix chain 'M' and resid 477 through 491 removed outlier: 4.484A pdb=" N ALA M 483 " --> pdb=" O THR M 479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 485 " --> pdb=" O ARG M 481 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 28 Processing helix chain 'N' and resid 44 through 56 removed outlier: 4.034A pdb=" N THR N 48 " --> pdb=" O ASP N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 90 through 92 No H-bonds generated for 'chain 'N' and resid 90 through 92' Processing helix chain 'N' and resid 109 through 114 removed outlier: 3.793A pdb=" N VAL N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 114 " --> pdb=" O ILE N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 114' Processing helix chain 'N' and resid 123 through 133 Processing helix chain 'N' and resid 149 through 157 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'N' and resid 222 through 226 removed outlier: 4.334A pdb=" N HIS N 225 " --> pdb=" O ASP N 222 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 233 removed outlier: 4.092A pdb=" N THR N 232 " --> pdb=" O LYS N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 248 Processing helix chain 'N' and resid 257 through 280 Processing helix chain 'N' and resid 300 through 304 removed outlier: 4.100A pdb=" N ASP N 303 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 365 removed outlier: 3.696A pdb=" N GLN N 357 " --> pdb=" O SER N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 385 removed outlier: 3.545A pdb=" N SER N 385 " --> pdb=" O ILE N 381 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 438 removed outlier: 3.588A pdb=" N GLU N 425 " --> pdb=" O GLU N 421 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU N 438 " --> pdb=" O ASN N 434 " (cutoff:3.500A) Processing helix chain 'N' and resid 442 through 447 removed outlier: 3.542A pdb=" N LEU N 446 " --> pdb=" O ASP N 442 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 450 No H-bonds generated for 'chain 'N' and resid 448 through 450' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 3.515A pdb=" N LEU A 420 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.493A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.706A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 33 removed outlier: 5.962A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS B 4 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 59 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE B 95 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE B 60 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 62 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.682A pdb=" N ILE B 241 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 286 removed outlier: 3.700A pdb=" N ARG B 283 " --> pdb=" O TRP B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB2, first strand: chain 'B' and resid 391 through 393 removed outlier: 3.727A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 393 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 401 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.560A pdb=" N GLY F 412 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F 169 " --> pdb=" O GLY F 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 95 removed outlier: 5.892A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 300 through 304 removed outlier: 6.571A pdb=" N VAL E 357 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL E 386 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE E 359 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE E 388 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA E 361 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.751A pdb=" N VAL E 426 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 32 through 34 removed outlier: 5.732A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS F 4 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE F 60 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE F 6 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE F 62 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER F 8 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER F 64 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 178 through 180 removed outlier: 7.554A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE F 403 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AC2, first strand: chain 'F' and resid 283 through 286 removed outlier: 3.591A pdb=" N TRP F 294 " --> pdb=" O ARG F 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 311 through 314 removed outlier: 3.577A pdb=" N MET F 336 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 328 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 334 " --> pdb=" O LYS F 328 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 397 through 398 removed outlier: 6.209A pdb=" N LYS J 167 " --> pdb=" O MET J 414 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET J 414 " --> pdb=" O LYS J 167 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS J 413 " --> pdb=" O LEU I 4 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TYR I 6 " --> pdb=" O LYS J 413 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N SER J 415 " --> pdb=" O TYR I 6 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AC6, first strand: chain 'I' and resid 92 through 95 removed outlier: 6.495A pdb=" N GLY I 42 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE I 142 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL I 44 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP I 139 " --> pdb=" O GLN I 222 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU I 224 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL I 141 " --> pdb=" O LEU I 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 301 through 304 removed outlier: 3.608A pdb=" N PHE I 304 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS I 279 " --> pdb=" O GLU I 356 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL I 357 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL I 386 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE I 359 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE I 388 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA I 361 " --> pdb=" O ILE I 388 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 420 " --> pdb=" O ILE I 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE I 443 " --> pdb=" O ALA I 418 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA I 418 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE I 419 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE I 412 " --> pdb=" O PHE I 419 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 425 through 426 removed outlier: 3.609A pdb=" N SER I 431 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 32 through 33 removed outlier: 5.808A pdb=" N ILE J 5 " --> pdb=" O TRP J 33 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYS J 4 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE J 60 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE J 6 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE J 62 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER J 8 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE J 95 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE J 60 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE J 118 " --> pdb=" O ILE J 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'J' and resid 334 through 335 removed outlier: 7.561A pdb=" N LEU J 402 " --> pdb=" O ILE J 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE J 401 " --> pdb=" O LEU J 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE J 403 " --> pdb=" O ILE J 391 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 184 through 186 removed outlier: 3.706A pdb=" N ILE J 241 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 207 through 210 removed outlier: 3.571A pdb=" N TYR J 210 " --> pdb=" O TYR J 213 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 283 through 286 removed outlier: 4.056A pdb=" N ARG J 283 " --> pdb=" O TRP J 294 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP J 294 " --> pdb=" O ARG J 283 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR J 293 " --> pdb=" O ILE J 323 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE J 323 " --> pdb=" O TYR J 293 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 283 through 286 removed outlier: 4.056A pdb=" N ARG J 283 " --> pdb=" O TRP J 294 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP J 294 " --> pdb=" O ARG J 283 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR J 293 " --> pdb=" O ILE J 323 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE J 323 " --> pdb=" O TYR J 293 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 5 through 6 removed outlier: 6.937A pdb=" N GLY M 385 " --> pdb=" O ASN M 446 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N CYS M 279 " --> pdb=" O PHE M 358 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS M 360 " --> pdb=" O CYS M 279 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 19 through 20 removed outlier: 3.705A pdb=" N LYS M 270 " --> pdb=" O LEU M 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 92 through 95 removed outlier: 3.750A pdb=" N GLY M 45 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL M 141 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 397 through 398 removed outlier: 3.589A pdb=" N GLU N 169 " --> pdb=" O GLY N 412 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.073A pdb=" N ILE N 5 " --> pdb=" O TRP N 33 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS N 4 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU N 61 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE N 6 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL N 63 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER N 8 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE N 118 " --> pdb=" O ILE N 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 176 through 177 removed outlier: 3.756A pdb=" N VAL N 334 " --> pdb=" O LYS N 328 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS N 328 " --> pdb=" O VAL N 334 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 208 through 210 removed outlier: 3.599A pdb=" N ILE N 208 " --> pdb=" O CYS N 215 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG N 186 " --> pdb=" O THR N 216 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 284 through 286 removed outlier: 3.609A pdb=" N ALA N 292 " --> pdb=" O TYR N 285 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 311 through 314 removed outlier: 3.524A pdb=" N THR N 344 " --> pdb=" O TYR N 318 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7993 1.33 - 1.45: 8059 1.45 - 1.57: 18488 1.57 - 1.69: 352 1.69 - 1.81: 140 Bond restraints: 35032 Sorted by residual: bond pdb=" CB ASN N 435 " pdb=" CG ASN N 435 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.99e+00 bond pdb=" CB MET M 406 " pdb=" CG MET M 406 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB ASN M 90 " pdb=" CG ASN M 90 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.58e+00 bond pdb=" CB ASN B 435 " pdb=" CG ASN B 435 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.20e+00 bond pdb=" CE LYS I 325 " pdb=" NZ LYS I 325 " ideal model delta sigma weight residual 1.489 1.445 0.044 3.00e-02 1.11e+03 2.15e+00 ... (remaining 35027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 47980 3.92 - 7.84: 150 7.84 - 11.77: 26 11.77 - 15.69: 3 15.69 - 19.61: 1 Bond angle restraints: 48160 Sorted by residual: angle pdb=" CA LEU I 210 " pdb=" CB LEU I 210 " pdb=" CG LEU I 210 " ideal model delta sigma weight residual 116.30 135.91 -19.61 3.50e+00 8.16e-02 3.14e+01 angle pdb=" CA MET F 277 " pdb=" CB MET F 277 " pdb=" CG MET F 277 " ideal model delta sigma weight residual 114.10 124.38 -10.28 2.00e+00 2.50e-01 2.64e+01 angle pdb=" CA MET F 92 " pdb=" CB MET F 92 " pdb=" CG MET F 92 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA LEU N 268 " pdb=" CB LEU N 268 " pdb=" CG LEU N 268 " ideal model delta sigma weight residual 116.30 131.48 -15.18 3.50e+00 8.16e-02 1.88e+01 angle pdb=" CA GLU I 488 " pdb=" CB GLU I 488 " pdb=" CG GLU I 488 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 ... (remaining 48155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 16802 18.17 - 36.33: 2827 36.33 - 54.50: 1017 54.50 - 72.67: 280 72.67 - 90.84: 50 Dihedral angle restraints: 20976 sinusoidal: 10196 harmonic: 10780 Sorted by residual: dihedral pdb=" CA MET M 406 " pdb=" C MET M 406 " pdb=" N ARG M 407 " pdb=" CA ARG M 407 " ideal model delta harmonic sigma weight residual 180.00 148.05 31.95 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA VAL E 317 " pdb=" C VAL E 317 " pdb=" N GLY E 318 " pdb=" CA GLY E 318 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA VAL I 317 " pdb=" C VAL I 317 " pdb=" N GLY I 318 " pdb=" CA GLY I 318 " ideal model delta harmonic sigma weight residual 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 20973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4785 0.080 - 0.160: 476 0.160 - 0.240: 14 0.240 - 0.320: 0 0.320 - 0.400: 1 Chirality restraints: 5276 Sorted by residual: chirality pdb=" CB ILE F 433 " pdb=" CA ILE F 433 " pdb=" CG1 ILE F 433 " pdb=" CG2 ILE F 433 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA TYR F 330 " pdb=" N TYR F 330 " pdb=" C TYR F 330 " pdb=" CB TYR F 330 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 49 " pdb=" CA ILE B 49 " pdb=" CG1 ILE B 49 " pdb=" CG2 ILE B 49 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 5273 not shown) Planarity restraints: 5488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO E 332 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 143 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO I 144 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 144 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 144 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 362 " 0.237 9.50e-02 1.11e+02 1.06e-01 7.27e+00 pdb=" NE ARG I 362 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG I 362 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 362 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 362 " 0.012 2.00e-02 2.50e+03 ... (remaining 5485 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4275 2.75 - 3.29: 33488 3.29 - 3.82: 61314 3.82 - 4.36: 68151 4.36 - 4.90: 111853 Nonbonded interactions: 279081 Sorted by model distance: nonbonded pdb=" OG SER N 359 " pdb=" OP1 DA O 44 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN I 90 " pdb=" OH TYR M 37 " model vdw 2.227 3.040 nonbonded pdb=" O4 DT C 26 " pdb=" O6 G D 20 " model vdw 2.230 2.432 nonbonded pdb=" O4 DT K 26 " pdb=" O6 G L 20 " model vdw 2.231 2.432 nonbonded pdb=" OH TYR J 221 " pdb=" O GLU J 231 " model vdw 2.235 3.040 ... (remaining 279076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' 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: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 32.430 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 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 0.051 35032 Z= 0.221 Angle : 0.727 19.610 48160 Z= 0.381 Chirality : 0.046 0.400 5276 Planarity : 0.006 0.106 5488 Dihedral : 20.585 90.836 14008 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.21 % Allowed : 31.22 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 3636 helix: -0.73 (0.13), residues: 1278 sheet: -1.36 (0.22), residues: 554 loop : -1.89 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 362 TYR 0.013 0.001 TYR M 285 PHE 0.024 0.001 PHE B 273 TRP 0.017 0.001 TRP I 86 HIS 0.012 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00484 (35032) covalent geometry : angle 0.72674 (48160) hydrogen bonds : bond 0.19052 ( 1128) hydrogen bonds : angle 7.74851 ( 3145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 770 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.6354 (tp) cc_final: 0.6139 (tp) REVERT: A 262 TYR cc_start: 0.7317 (t80) cc_final: 0.7045 (t80) REVERT: E 117 LEU cc_start: 0.6976 (tp) cc_final: 0.6674 (tt) REVERT: E 430 GLN cc_start: 0.4080 (mm-40) cc_final: 0.3765 (tm-30) REVERT: I 422 THR cc_start: 0.7126 (p) cc_final: 0.6919 (p) REVERT: I 474 ASP cc_start: 0.3166 (t0) cc_final: 0.1677 (t0) REVERT: J 433 ILE cc_start: 0.7281 (pt) cc_final: 0.7017 (mt) REVERT: M 304 PHE cc_start: 0.5424 (m-10) cc_final: 0.5204 (m-10) REVERT: M 474 ASP cc_start: 0.5104 (t0) cc_final: 0.4058 (t0) REVERT: N 345 MET cc_start: 0.6063 (ppp) cc_final: 0.5799 (tmm) outliers start: 7 outliers final: 1 residues processed: 776 average time/residue: 0.2371 time to fit residues: 287.5353 Evaluate side-chains 590 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 5.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 251 HIS A 341 GLN B 349 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 374 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS I 111 HIS I 430 GLN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN J 357 GLN M 35 GLN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN N 69 ASN N 234 ASN N 258 ASN N 320 HIS ** N 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.194626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.162502 restraints weight = 70727.568| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 4.32 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35032 Z= 0.139 Angle : 0.651 13.263 48160 Z= 0.345 Chirality : 0.044 0.337 5276 Planarity : 0.005 0.065 5488 Dihedral : 18.565 82.227 6389 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.38 % Allowed : 29.91 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3636 helix: -0.31 (0.14), residues: 1319 sheet: -1.40 (0.21), residues: 572 loop : -1.79 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 24 TYR 0.022 0.001 TYR E 346 PHE 0.024 0.001 PHE N 411 TRP 0.021 0.002 TRP F 294 HIS 0.011 0.001 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00313 (35032) covalent geometry : angle 0.65132 (48160) hydrogen bonds : bond 0.04010 ( 1128) hydrogen bonds : angle 5.84708 ( 3145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 667 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.6593 (tp) cc_final: 0.6262 (tp) REVERT: A 117 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6782 (mt) REVERT: A 225 ARG cc_start: 0.7367 (ttm110) cc_final: 0.6996 (ttp-110) REVERT: A 251 HIS cc_start: 0.5662 (OUTLIER) cc_final: 0.5337 (m90) REVERT: A 262 TYR cc_start: 0.8190 (t80) cc_final: 0.7503 (t80) REVERT: A 305 LEU cc_start: 0.7675 (pp) cc_final: 0.7382 (tt) REVERT: A 383 LEU cc_start: 0.8351 (pt) cc_final: 0.8012 (pt) REVERT: B 14 ASP cc_start: 0.7705 (t0) cc_final: 0.7231 (t0) REVERT: B 37 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6933 (pp) REVERT: B 275 LEU cc_start: 0.8335 (mt) cc_final: 0.7364 (mt) REVERT: E 117 LEU cc_start: 0.6968 (tp) cc_final: 0.6712 (tt) REVERT: E 149 LYS cc_start: 0.6809 (tptt) cc_final: 0.6362 (tppt) REVERT: E 205 GLN cc_start: 0.6724 (tm-30) cc_final: 0.6420 (tm-30) REVERT: F 233 TYR cc_start: 0.5829 (t80) cc_final: 0.5251 (t80) REVERT: F 240 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6958 (mtm-85) REVERT: F 265 ILE cc_start: 0.9092 (mt) cc_final: 0.8888 (tp) REVERT: F 294 TRP cc_start: 0.6201 (p-90) cc_final: 0.5661 (p-90) REVERT: F 319 TRP cc_start: 0.7943 (p-90) cc_final: 0.6980 (p-90) REVERT: F 402 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7948 (pp) REVERT: I 118 VAL cc_start: 0.7728 (t) cc_final: 0.7443 (p) REVERT: I 397 TYR cc_start: 0.5538 (m-10) cc_final: 0.5121 (m-10) REVERT: I 398 LYS cc_start: 0.6859 (tptt) cc_final: 0.6535 (tptt) REVERT: J 181 PHE cc_start: 0.8268 (t80) cc_final: 0.8028 (t80) REVERT: J 188 HIS cc_start: 0.5521 (m-70) cc_final: 0.5037 (m90) REVERT: J 271 LYS cc_start: 0.9133 (tptt) cc_final: 0.8819 (tptt) REVERT: J 274 GLU cc_start: 0.8382 (pp20) cc_final: 0.8129 (pp20) REVERT: J 374 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7184 (ttt-90) REVERT: J 433 ILE cc_start: 0.7121 (pt) cc_final: 0.6847 (mt) REVERT: M 79 GLU cc_start: 0.7800 (pm20) cc_final: 0.7558 (mp0) REVERT: M 97 THR cc_start: 0.8412 (p) cc_final: 0.8183 (t) REVERT: M 148 TYR cc_start: 0.7202 (t80) cc_final: 0.6941 (t80) REVERT: M 384 VAL cc_start: 0.8434 (t) cc_final: 0.7934 (m) REVERT: M 435 MET cc_start: 0.7178 (tmm) cc_final: 0.6502 (tmm) REVERT: M 481 ARG cc_start: 0.6033 (ttt180) cc_final: 0.5709 (ttt-90) REVERT: M 503 PHE cc_start: 0.5016 (t80) cc_final: 0.4806 (t80) REVERT: N 22 SER cc_start: 0.9090 (m) cc_final: 0.8831 (t) REVERT: N 158 PHE cc_start: 0.4730 (t80) cc_final: 0.4476 (t80) REVERT: N 318 TYR cc_start: 0.3379 (OUTLIER) cc_final: 0.3069 (m-80) outliers start: 111 outliers final: 44 residues processed: 728 average time/residue: 0.2197 time to fit residues: 254.6958 Evaluate side-chains 651 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 602 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 258 ASN Chi-restraints excluded: chain N residue 271 LYS Chi-restraints excluded: chain N residue 318 TYR Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 327 optimal weight: 0.6980 chunk 329 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 353 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 151 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN B 320 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN F 320 HIS I 111 HIS I 349 GLN ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN J 314 GLN M 35 GLN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN N 262 GLN N 270 ASN N 349 ASN N 405 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.193381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.161342 restraints weight = 70636.030| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 4.30 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35032 Z= 0.129 Angle : 0.620 12.416 48160 Z= 0.327 Chirality : 0.043 0.315 5276 Planarity : 0.005 0.065 5488 Dihedral : 18.552 84.399 6388 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.39 % Allowed : 29.39 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3636 helix: -0.14 (0.14), residues: 1313 sheet: -1.45 (0.23), residues: 488 loop : -1.69 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 283 TYR 0.021 0.001 TYR E 6 PHE 0.019 0.001 PHE N 205 TRP 0.015 0.001 TRP I 86 HIS 0.025 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00288 (35032) covalent geometry : angle 0.61967 (48160) hydrogen bonds : bond 0.03801 ( 1128) hydrogen bonds : angle 5.48312 ( 3145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 640 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.6461 (tp) cc_final: 0.6148 (tp) REVERT: A 87 GLU cc_start: 0.6644 (mp0) cc_final: 0.6297 (mp0) REVERT: A 100 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: A 117 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6915 (mt) REVERT: A 225 ARG cc_start: 0.7300 (ttm110) cc_final: 0.7060 (ttp-110) REVERT: A 262 TYR cc_start: 0.8185 (t80) cc_final: 0.7528 (t80) REVERT: A 383 LEU cc_start: 0.8348 (pt) cc_final: 0.8040 (pt) REVERT: A 458 ASP cc_start: 0.7308 (m-30) cc_final: 0.7094 (m-30) REVERT: A 485 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6478 (tmtt) REVERT: B 14 ASP cc_start: 0.7815 (t0) cc_final: 0.7214 (t0) REVERT: B 37 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6860 (pp) REVERT: E 24 ARG cc_start: 0.6105 (mpp80) cc_final: 0.5533 (mtm180) REVERT: E 50 LEU cc_start: 0.7383 (mt) cc_final: 0.7052 (mt) REVERT: E 59 LYS cc_start: 0.7124 (mmmm) cc_final: 0.6789 (mtmm) REVERT: E 74 MET cc_start: 0.6377 (pmm) cc_final: 0.6163 (pmm) REVERT: E 353 TYR cc_start: 0.7583 (m-80) cc_final: 0.7363 (m-80) REVERT: F 13 GLU cc_start: 0.7181 (mp0) cc_final: 0.6658 (mp0) REVERT: F 89 GLN cc_start: 0.7448 (pm20) cc_final: 0.7219 (pm20) REVERT: F 119 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7822 (p0) REVERT: F 135 PHE cc_start: 0.5636 (OUTLIER) cc_final: 0.5167 (t80) REVERT: F 205 PHE cc_start: 0.7006 (m-80) cc_final: 0.6800 (m-80) REVERT: F 294 TRP cc_start: 0.6232 (p-90) cc_final: 0.5595 (p-90) REVERT: F 382 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7627 (mpt180) REVERT: F 402 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7889 (pp) REVERT: I 8 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: I 397 TYR cc_start: 0.5347 (m-10) cc_final: 0.5100 (m-10) REVERT: I 398 LYS cc_start: 0.7132 (tptt) cc_final: 0.6884 (tptt) REVERT: I 474 ASP cc_start: 0.3588 (t0) cc_final: 0.2349 (t0) REVERT: I 476 GLU cc_start: 0.7540 (pm20) cc_final: 0.7256 (pm20) REVERT: I 488 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6627 (pm20) REVERT: J 86 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8690 (mtpt) REVERT: J 138 GLN cc_start: 0.6888 (mp10) cc_final: 0.6682 (mp10) REVERT: J 181 PHE cc_start: 0.8355 (t80) cc_final: 0.8028 (t80) REVERT: J 219 TRP cc_start: 0.5516 (m-90) cc_final: 0.4886 (m-90) REVERT: J 270 ASN cc_start: 0.9174 (t0) cc_final: 0.8942 (t0) REVERT: J 271 LYS cc_start: 0.9213 (tptt) cc_final: 0.8869 (tptt) REVERT: J 374 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.7415 (ttt-90) REVERT: J 433 ILE cc_start: 0.7028 (pt) cc_final: 0.6811 (mt) REVERT: M 97 THR cc_start: 0.8405 (p) cc_final: 0.8176 (t) REVERT: M 148 TYR cc_start: 0.7279 (t80) cc_final: 0.6992 (t80) REVERT: M 209 GLN cc_start: 0.8258 (pt0) cc_final: 0.8049 (pt0) REVERT: M 384 VAL cc_start: 0.8408 (t) cc_final: 0.7930 (m) REVERT: M 386 VAL cc_start: 0.7994 (t) cc_final: 0.7590 (m) REVERT: M 435 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6518 (tmm) REVERT: M 436 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: M 481 ARG cc_start: 0.6103 (ttt180) cc_final: 0.5825 (ttt-90) REVERT: N 22 SER cc_start: 0.9137 (m) cc_final: 0.8870 (t) REVERT: N 158 PHE cc_start: 0.4862 (t80) cc_final: 0.4470 (t80) REVERT: N 233 TYR cc_start: 0.6875 (t80) cc_final: 0.6490 (t80) REVERT: N 414 MET cc_start: 0.6589 (mmm) cc_final: 0.5965 (mmm) outliers start: 144 outliers final: 67 residues processed: 724 average time/residue: 0.2258 time to fit residues: 260.2499 Evaluate side-chains 668 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 589 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 LYS Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 320 HIS Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 35 GLN Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 435 MET Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 496 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 349 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 163 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 350 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 366 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 251 HIS A 302 GLN A 350 ASN A 454 GLN A 466 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 251 HIS E 430 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN M 61 GLN M 68 ASN M 251 HIS ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.184385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.151812 restraints weight = 68895.601| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 4.25 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 35032 Z= 0.199 Angle : 0.681 12.663 48160 Z= 0.360 Chirality : 0.046 0.414 5276 Planarity : 0.005 0.060 5488 Dihedral : 18.638 84.744 6388 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.46 % Allowed : 29.60 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 3636 helix: -0.04 (0.14), residues: 1280 sheet: -1.41 (0.22), residues: 536 loop : -1.67 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 382 TYR 0.022 0.002 TYR E 262 PHE 0.031 0.002 PHE N 411 TRP 0.023 0.002 TRP I 86 HIS 0.027 0.002 HIS I 111 Details of bonding type rmsd covalent geometry : bond 0.00460 (35032) covalent geometry : angle 0.68099 (48160) hydrogen bonds : bond 0.04241 ( 1128) hydrogen bonds : angle 5.38131 ( 3145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 647 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8032 (mttt) cc_final: 0.7726 (mttp) REVERT: A 64 ILE cc_start: 0.6563 (tp) cc_final: 0.6204 (tp) REVERT: A 87 GLU cc_start: 0.6916 (mp0) cc_final: 0.6552 (mp0) REVERT: A 100 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6035 (pt0) REVERT: A 117 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7077 (mt) REVERT: A 136 VAL cc_start: 0.8365 (t) cc_final: 0.8144 (t) REVERT: A 146 GLU cc_start: 0.7392 (pm20) cc_final: 0.7029 (tp30) REVERT: A 225 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7417 (ttp-110) REVERT: A 251 HIS cc_start: 0.5768 (OUTLIER) cc_final: 0.5419 (m90) REVERT: A 262 TYR cc_start: 0.8401 (t80) cc_final: 0.7971 (t80) REVERT: A 458 ASP cc_start: 0.7381 (m-30) cc_final: 0.7176 (m-30) REVERT: A 485 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6463 (tmtt) REVERT: B 14 ASP cc_start: 0.8556 (t0) cc_final: 0.8203 (t0) REVERT: B 352 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8399 (mmtm) REVERT: B 372 LYS cc_start: 0.8335 (tptp) cc_final: 0.8082 (tptp) REVERT: B 376 LYS cc_start: 0.7745 (mttm) cc_final: 0.7016 (mttm) REVERT: E 59 LYS cc_start: 0.7157 (mmmm) cc_final: 0.6904 (mtmm) REVERT: E 74 MET cc_start: 0.6155 (pmm) cc_final: 0.5815 (pmm) REVERT: E 205 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6946 (tm-30) REVERT: E 296 ASN cc_start: 0.5910 (m-40) cc_final: 0.5645 (m-40) REVERT: E 364 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.5780 (mtm-85) REVERT: E 488 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7458 (mt-10) REVERT: F 13 GLU cc_start: 0.7369 (mp0) cc_final: 0.6666 (mp0) REVERT: F 89 GLN cc_start: 0.8161 (pm20) cc_final: 0.7763 (pm20) REVERT: F 111 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7426 (mm-30) REVERT: F 135 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5192 (t80) REVERT: F 161 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.5355 (m-30) REVERT: F 205 PHE cc_start: 0.7133 (m-80) cc_final: 0.6885 (m-80) REVERT: F 240 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6805 (mpp80) REVERT: F 250 ARG cc_start: 0.8084 (tpm170) cc_final: 0.7545 (tpm170) REVERT: F 294 TRP cc_start: 0.6343 (p-90) cc_final: 0.5715 (p-90) REVERT: F 336 MET cc_start: 0.5670 (mpp) cc_final: 0.5350 (mpp) REVERT: F 373 TRP cc_start: 0.8068 (m100) cc_final: 0.7853 (m100) REVERT: F 382 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7797 (mmt-90) REVERT: F 402 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8092 (pp) REVERT: I 8 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: I 35 GLN cc_start: 0.6424 (tp40) cc_final: 0.5905 (tp40) REVERT: I 85 LYS cc_start: 0.6863 (pptt) cc_final: 0.6636 (pptt) REVERT: I 397 TYR cc_start: 0.5679 (m-10) cc_final: 0.5117 (m-10) REVERT: I 444 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7357 (tm-30) REVERT: I 476 GLU cc_start: 0.7526 (pm20) cc_final: 0.7076 (pm20) REVERT: I 488 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: J 13 GLU cc_start: 0.8090 (mp0) cc_final: 0.7799 (mp0) REVERT: J 86 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8745 (mtpt) REVERT: J 130 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6398 (p0) REVERT: J 159 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7703 (tt) REVERT: J 181 PHE cc_start: 0.8353 (t80) cc_final: 0.8047 (t80) REVERT: J 211 LYS cc_start: 0.6585 (mttt) cc_final: 0.5611 (mmmt) REVERT: J 219 TRP cc_start: 0.6107 (m-90) cc_final: 0.5344 (m-90) REVERT: J 271 LYS cc_start: 0.9171 (tptt) cc_final: 0.8880 (tptt) REVERT: J 274 GLU cc_start: 0.8471 (pp20) cc_final: 0.8131 (pp20) REVERT: J 362 ARG cc_start: 0.3226 (OUTLIER) cc_final: 0.2408 (mmp-170) REVERT: J 370 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6000 (p0) REVERT: J 374 ARG cc_start: 0.7855 (ttt-90) cc_final: 0.7501 (ttt-90) REVERT: J 445 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.4739 (mm-30) REVERT: M 82 PHE cc_start: 0.8323 (m-10) cc_final: 0.7848 (m-10) REVERT: M 97 THR cc_start: 0.8507 (p) cc_final: 0.8306 (t) REVERT: M 150 TYR cc_start: 0.5865 (t80) cc_final: 0.5497 (t80) REVERT: M 384 VAL cc_start: 0.8416 (t) cc_final: 0.8091 (m) REVERT: M 386 VAL cc_start: 0.8266 (t) cc_final: 0.7952 (m) REVERT: M 436 GLU cc_start: 0.6782 (mp0) cc_final: 0.6213 (mp0) REVERT: M 503 PHE cc_start: 0.6100 (t80) cc_final: 0.5753 (t80) REVERT: N 409 LYS cc_start: 0.6682 (mttt) cc_final: 0.6432 (mmtp) REVERT: N 414 MET cc_start: 0.7041 (mmm) cc_final: 0.6404 (mmm) outliers start: 179 outliers final: 96 residues processed: 749 average time/residue: 0.2224 time to fit residues: 266.8230 Evaluate side-chains 716 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 604 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 258 ASN Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 285 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 322 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS J 270 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.183219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.150668 restraints weight = 69483.112| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 4.32 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35032 Z= 0.177 Angle : 0.670 12.505 48160 Z= 0.352 Chirality : 0.045 0.275 5276 Planarity : 0.005 0.058 5488 Dihedral : 18.681 85.957 6388 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.06 % Allowed : 31.22 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.13), residues: 3636 helix: -0.04 (0.14), residues: 1282 sheet: -1.39 (0.22), residues: 532 loop : -1.71 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 283 TYR 0.027 0.002 TYR M 285 PHE 0.023 0.002 PHE A 442 TRP 0.020 0.002 TRP I 320 HIS 0.054 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00412 (35032) covalent geometry : angle 0.67019 (48160) hydrogen bonds : bond 0.04095 ( 1128) hydrogen bonds : angle 5.33212 ( 3145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 627 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8059 (mttt) cc_final: 0.7757 (mttp) REVERT: A 64 ILE cc_start: 0.6389 (tp) cc_final: 0.6124 (tp) REVERT: A 85 LYS cc_start: 0.7838 (ptpp) cc_final: 0.7547 (ttpp) REVERT: A 87 GLU cc_start: 0.6999 (mp0) cc_final: 0.6441 (mm-30) REVERT: A 100 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6196 (pt0) REVERT: A 117 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7112 (mt) REVERT: A 136 VAL cc_start: 0.8415 (t) cc_final: 0.8184 (t) REVERT: A 225 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7457 (ttp-110) REVERT: A 262 TYR cc_start: 0.8390 (t80) cc_final: 0.7975 (t80) REVERT: B 14 ASP cc_start: 0.8620 (t0) cc_final: 0.8204 (t0) REVERT: B 16 ASP cc_start: 0.8237 (p0) cc_final: 0.7921 (p0) REVERT: B 219 TRP cc_start: 0.6663 (m100) cc_final: 0.5172 (m100) REVERT: B 279 ASP cc_start: 0.8371 (m-30) cc_final: 0.7852 (m-30) REVERT: B 283 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7361 (mmm160) REVERT: B 308 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5902 (tp) REVERT: B 352 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8497 (mmtm) REVERT: B 372 LYS cc_start: 0.8602 (tptp) cc_final: 0.8242 (tptt) REVERT: E 50 LEU cc_start: 0.7423 (mt) cc_final: 0.7066 (mt) REVERT: E 59 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6899 (mtmm) REVERT: E 72 ARG cc_start: 0.6836 (mpp80) cc_final: 0.6273 (mtt90) REVERT: E 74 MET cc_start: 0.6150 (pmm) cc_final: 0.5783 (pmm) REVERT: E 286 LYS cc_start: 0.7931 (tptp) cc_final: 0.7681 (tppt) REVERT: E 296 ASN cc_start: 0.6039 (m-40) cc_final: 0.5751 (m-40) REVERT: E 364 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.5886 (mtm-85) REVERT: E 458 ASP cc_start: 0.7964 (m-30) cc_final: 0.7639 (t0) REVERT: E 476 GLU cc_start: 0.7369 (pm20) cc_final: 0.6898 (pm20) REVERT: E 503 PHE cc_start: 0.5795 (OUTLIER) cc_final: 0.4156 (t80) REVERT: F 89 GLN cc_start: 0.8329 (pm20) cc_final: 0.7852 (pm20) REVERT: F 111 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7399 (mm-30) REVERT: F 119 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8197 (p0) REVERT: F 122 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7934 (pttp) REVERT: F 135 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.5051 (t80) REVERT: F 220 GLU cc_start: 0.7696 (mp0) cc_final: 0.7203 (mp0) REVERT: F 233 TYR cc_start: 0.6076 (t80) cc_final: 0.5700 (t80) REVERT: F 324 SER cc_start: 0.8269 (t) cc_final: 0.7701 (p) REVERT: F 382 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7802 (mmt-90) REVERT: I 35 GLN cc_start: 0.6567 (tp40) cc_final: 0.6210 (tp40) REVERT: I 85 LYS cc_start: 0.7308 (pttt) cc_final: 0.6926 (pptt) REVERT: I 400 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: I 444 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7279 (tm-30) REVERT: I 476 GLU cc_start: 0.7639 (pm20) cc_final: 0.7272 (pm20) REVERT: I 488 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: J 13 GLU cc_start: 0.8139 (mp0) cc_final: 0.7768 (mp0) REVERT: J 130 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6283 (p0) REVERT: J 159 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7775 (tt) REVERT: J 171 TYR cc_start: 0.7502 (m-80) cc_final: 0.7040 (m-80) REVERT: J 181 PHE cc_start: 0.8463 (t80) cc_final: 0.8129 (t80) REVERT: J 211 LYS cc_start: 0.6695 (mttt) cc_final: 0.5792 (mmmt) REVERT: J 219 TRP cc_start: 0.6386 (m-90) cc_final: 0.5734 (m-90) REVERT: J 271 LYS cc_start: 0.9204 (tptt) cc_final: 0.8853 (tptt) REVERT: J 433 ILE cc_start: 0.7227 (pt) cc_final: 0.6894 (mt) REVERT: M 97 THR cc_start: 0.8526 (p) cc_final: 0.8262 (t) REVERT: M 148 TYR cc_start: 0.7282 (t80) cc_final: 0.7040 (t80) REVERT: M 150 TYR cc_start: 0.5901 (t80) cc_final: 0.5551 (t80) REVERT: M 358 PHE cc_start: 0.7382 (m-10) cc_final: 0.6871 (m-10) REVERT: M 382 ASN cc_start: 0.7734 (m-40) cc_final: 0.7489 (m-40) REVERT: M 384 VAL cc_start: 0.8515 (t) cc_final: 0.7699 (m) REVERT: M 386 VAL cc_start: 0.8290 (t) cc_final: 0.8001 (m) REVERT: M 435 MET cc_start: 0.7521 (tmm) cc_final: 0.6942 (tmm) REVERT: M 436 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: M 481 ARG cc_start: 0.6314 (ttt180) cc_final: 0.5847 (ttt-90) REVERT: N 83 LYS cc_start: 0.8308 (tppp) cc_final: 0.8069 (mmmm) REVERT: N 90 ASP cc_start: 0.7585 (t70) cc_final: 0.7241 (p0) REVERT: N 152 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8254 (tp) REVERT: N 181 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5712 (p90) REVERT: N 321 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7702 (t80) REVERT: N 368 TRP cc_start: 0.7196 (p90) cc_final: 0.6488 (p90) REVERT: N 374 ARG cc_start: 0.7749 (ptt90) cc_final: 0.7430 (ptm-80) REVERT: N 409 LYS cc_start: 0.6685 (mttt) cc_final: 0.6434 (mmtp) REVERT: N 414 MET cc_start: 0.6950 (mmm) cc_final: 0.6425 (mmm) outliers start: 166 outliers final: 109 residues processed: 721 average time/residue: 0.2185 time to fit residues: 251.4703 Evaluate side-chains 723 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 597 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 258 ASN Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 429 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 256 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 327 optimal weight: 0.9990 chunk 344 optimal weight: 0.0370 chunk 195 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 251 optimal weight: 0.0050 chunk 87 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 354 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 GLN ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS J 270 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 HIS N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.187457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.155151 restraints weight = 69171.160| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 4.32 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35032 Z= 0.126 Angle : 0.638 15.239 48160 Z= 0.333 Chirality : 0.043 0.276 5276 Planarity : 0.005 0.061 5488 Dihedral : 18.623 87.988 6388 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.24 % Allowed : 31.80 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.13), residues: 3636 helix: 0.04 (0.14), residues: 1276 sheet: -1.31 (0.22), residues: 508 loop : -1.66 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 72 TYR 0.027 0.001 TYR E 285 PHE 0.031 0.001 PHE M 503 TRP 0.022 0.001 TRP F 294 HIS 0.009 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00286 (35032) covalent geometry : angle 0.63824 (48160) hydrogen bonds : bond 0.03505 ( 1128) hydrogen bonds : angle 5.16931 ( 3145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 623 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8126 (mttt) cc_final: 0.7683 (mttp) REVERT: A 85 LYS cc_start: 0.7623 (ptpp) cc_final: 0.7320 (ptmm) REVERT: A 100 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5915 (pt0) REVERT: A 117 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7161 (mt) REVERT: A 136 VAL cc_start: 0.8355 (t) cc_final: 0.8140 (t) REVERT: A 225 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7157 (ttp-110) REVERT: A 262 TYR cc_start: 0.8257 (t80) cc_final: 0.7676 (t80) REVERT: A 485 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.5960 (mmtt) REVERT: B 14 ASP cc_start: 0.8561 (t0) cc_final: 0.8089 (t0) REVERT: B 171 TYR cc_start: 0.7088 (m-80) cc_final: 0.6873 (m-80) REVERT: B 219 TRP cc_start: 0.6709 (m100) cc_final: 0.5677 (m100) REVERT: B 279 ASP cc_start: 0.8196 (m-30) cc_final: 0.7672 (m-30) REVERT: B 283 ARG cc_start: 0.7868 (mmm160) cc_final: 0.7410 (mmm160) REVERT: B 304 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7927 (mmmt) REVERT: B 352 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8614 (mmtm) REVERT: E 50 LEU cc_start: 0.7396 (mt) cc_final: 0.7033 (mt) REVERT: E 227 SER cc_start: 0.6411 (p) cc_final: 0.6087 (p) REVERT: E 364 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.5728 (mtm-85) REVERT: E 476 GLU cc_start: 0.7278 (pm20) cc_final: 0.6793 (pm20) REVERT: E 488 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7391 (mt-10) REVERT: E 503 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.4497 (t80) REVERT: F 13 GLU cc_start: 0.7411 (mp0) cc_final: 0.6921 (mp0) REVERT: F 72 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5493 (tm-30) REVERT: F 89 GLN cc_start: 0.8064 (pm20) cc_final: 0.7727 (pm20) REVERT: F 122 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7885 (pttp) REVERT: F 135 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5116 (t80) REVERT: F 240 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.7102 (mpp80) REVERT: F 324 SER cc_start: 0.8187 (t) cc_final: 0.7698 (p) REVERT: F 406 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8250 (mmmm) REVERT: I 8 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: I 35 GLN cc_start: 0.6532 (tp40) cc_final: 0.5983 (tp40) REVERT: I 85 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6933 (ptmm) REVERT: I 302 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5478 (mp10) REVERT: I 368 GLU cc_start: 0.8287 (pp20) cc_final: 0.7978 (pp20) REVERT: I 398 LYS cc_start: 0.7051 (tptt) cc_final: 0.6814 (tptt) REVERT: I 400 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: I 444 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7222 (tm-30) REVERT: I 474 ASP cc_start: 0.3788 (t0) cc_final: 0.2112 (t0) REVERT: I 476 GLU cc_start: 0.7565 (pm20) cc_final: 0.7180 (pm20) REVERT: I 488 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: J 13 GLU cc_start: 0.8112 (mp0) cc_final: 0.7761 (mp0) REVERT: J 86 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8665 (mtpt) REVERT: J 130 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6343 (p0) REVERT: J 181 PHE cc_start: 0.8409 (t80) cc_final: 0.8065 (t80) REVERT: J 211 LYS cc_start: 0.6677 (mttt) cc_final: 0.5881 (mmmt) REVERT: J 219 TRP cc_start: 0.6423 (m-90) cc_final: 0.5603 (m-90) REVERT: J 271 LYS cc_start: 0.9178 (tptt) cc_final: 0.8860 (tptt) REVERT: J 274 GLU cc_start: 0.8593 (pp20) cc_final: 0.8332 (pp20) REVERT: J 362 ARG cc_start: 0.3361 (OUTLIER) cc_final: 0.2438 (mmp-170) REVERT: M 97 THR cc_start: 0.8540 (p) cc_final: 0.8328 (t) REVERT: M 106 PHE cc_start: 0.0881 (OUTLIER) cc_final: 0.0146 (m-80) REVERT: M 150 TYR cc_start: 0.5819 (t80) cc_final: 0.5504 (t80) REVERT: M 249 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7854 (mm-30) REVERT: M 355 LYS cc_start: 0.6952 (mtmt) cc_final: 0.6449 (tptm) REVERT: M 358 PHE cc_start: 0.7323 (m-10) cc_final: 0.6906 (m-10) REVERT: M 382 ASN cc_start: 0.7713 (m-40) cc_final: 0.7442 (m-40) REVERT: M 384 VAL cc_start: 0.8493 (t) cc_final: 0.7688 (m) REVERT: M 386 VAL cc_start: 0.8200 (t) cc_final: 0.7928 (m) REVERT: M 435 MET cc_start: 0.7419 (tmm) cc_final: 0.6566 (tmm) REVERT: N 83 LYS cc_start: 0.8244 (tppp) cc_final: 0.8016 (mmmm) REVERT: N 107 ASP cc_start: 0.8050 (t70) cc_final: 0.7800 (t0) REVERT: N 181 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5748 (p90) REVERT: N 374 ARG cc_start: 0.7782 (ptt90) cc_final: 0.7431 (ptm-80) REVERT: N 409 LYS cc_start: 0.6546 (mttt) cc_final: 0.6297 (mmtp) REVERT: N 414 MET cc_start: 0.6583 (mmm) cc_final: 0.6033 (mmm) outliers start: 139 outliers final: 96 residues processed: 704 average time/residue: 0.2189 time to fit residues: 246.2679 Evaluate side-chains 711 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 598 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 302 GLN Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 45 PHE Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 6 optimal weight: 1.9990 chunk 292 optimal weight: 0.0070 chunk 277 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 40 optimal weight: 0.0000 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS E 61 GLN E 430 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 302 GLN ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 360 HIS ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.185759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.153363 restraints weight = 69787.615| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 4.32 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35032 Z= 0.137 Angle : 0.646 14.163 48160 Z= 0.336 Chirality : 0.044 0.231 5276 Planarity : 0.005 0.115 5488 Dihedral : 18.601 87.268 6388 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.51 % Allowed : 32.20 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.13), residues: 3636 helix: 0.09 (0.14), residues: 1266 sheet: -1.27 (0.23), residues: 504 loop : -1.65 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 113 TYR 0.023 0.001 TYR E 6 PHE 0.037 0.001 PHE N 205 TRP 0.047 0.002 TRP J 369 HIS 0.008 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00316 (35032) covalent geometry : angle 0.64592 (48160) hydrogen bonds : bond 0.03606 ( 1128) hydrogen bonds : angle 5.10939 ( 3145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 617 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8156 (mttt) cc_final: 0.7728 (mttp) REVERT: A 89 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: A 100 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5980 (pt0) REVERT: A 136 VAL cc_start: 0.8365 (t) cc_final: 0.8122 (t) REVERT: A 262 TYR cc_start: 0.8328 (t80) cc_final: 0.7825 (t80) REVERT: A 406 MET cc_start: 0.7152 (tmm) cc_final: 0.6799 (tmm) REVERT: A 435 MET cc_start: 0.7791 (tpp) cc_final: 0.7556 (tpp) REVERT: A 485 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6006 (mmtt) REVERT: B 14 ASP cc_start: 0.8660 (t0) cc_final: 0.8174 (t0) REVERT: B 105 TYR cc_start: 0.7145 (t80) cc_final: 0.6783 (t80) REVERT: B 171 TYR cc_start: 0.7062 (m-80) cc_final: 0.6760 (m-80) REVERT: B 219 TRP cc_start: 0.6765 (m100) cc_final: 0.5732 (m100) REVERT: B 279 ASP cc_start: 0.8236 (m-30) cc_final: 0.7746 (m-30) REVERT: B 283 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7499 (mmm160) REVERT: B 352 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8615 (mmtm) REVERT: E 85 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7330 (pttm) REVERT: E 227 SER cc_start: 0.6493 (p) cc_final: 0.6149 (p) REVERT: E 249 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7439 (tp30) REVERT: E 343 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8415 (pp) REVERT: E 364 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.5787 (mtm-85) REVERT: E 369 GLU cc_start: 0.8162 (pt0) cc_final: 0.7871 (pt0) REVERT: E 476 GLU cc_start: 0.7263 (pm20) cc_final: 0.6801 (pm20) REVERT: E 503 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.4536 (t80) REVERT: F 13 GLU cc_start: 0.7430 (mp0) cc_final: 0.6951 (mp0) REVERT: F 72 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5354 (tm-30) REVERT: F 89 GLN cc_start: 0.8208 (pm20) cc_final: 0.7841 (pm20) REVERT: F 111 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7511 (tp30) REVERT: F 122 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7941 (pttp) REVERT: F 135 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5011 (t80) REVERT: F 169 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6363 (mm-30) REVERT: F 289 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8681 (mmtm) REVERT: F 304 LYS cc_start: 0.8831 (tppt) cc_final: 0.8288 (mmmm) REVERT: F 324 SER cc_start: 0.8219 (t) cc_final: 0.7665 (p) REVERT: I 8 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: I 35 GLN cc_start: 0.6464 (tp40) cc_final: 0.6060 (tp40) REVERT: I 74 MET cc_start: 0.3210 (pmm) cc_final: 0.3004 (pmm) REVERT: I 85 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6946 (pptt) REVERT: I 368 GLU cc_start: 0.8336 (pp20) cc_final: 0.8027 (pp20) REVERT: I 398 LYS cc_start: 0.7023 (tptt) cc_final: 0.6477 (tptt) REVERT: I 400 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: I 444 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7161 (tm-30) REVERT: I 476 GLU cc_start: 0.7523 (pm20) cc_final: 0.7128 (pm20) REVERT: I 488 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: J 13 GLU cc_start: 0.8134 (mp0) cc_final: 0.7795 (mp0) REVERT: J 86 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8661 (mtpt) REVERT: J 130 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6347 (p0) REVERT: J 181 PHE cc_start: 0.8445 (t80) cc_final: 0.7945 (t80) REVERT: J 211 LYS cc_start: 0.6707 (mttt) cc_final: 0.5916 (mmmt) REVERT: J 219 TRP cc_start: 0.6584 (m-90) cc_final: 0.5782 (m-90) REVERT: J 271 LYS cc_start: 0.9210 (tptt) cc_final: 0.8823 (tptt) REVERT: J 362 ARG cc_start: 0.3350 (OUTLIER) cc_final: 0.2414 (mmp-170) REVERT: J 401 ILE cc_start: 0.7829 (mm) cc_final: 0.7584 (tp) REVERT: M 97 THR cc_start: 0.8575 (p) cc_final: 0.8313 (t) REVERT: M 102 ARG cc_start: 0.8217 (tpm170) cc_final: 0.8008 (tpm170) REVERT: M 106 PHE cc_start: 0.0882 (OUTLIER) cc_final: -0.0057 (m-80) REVERT: M 150 TYR cc_start: 0.5839 (t80) cc_final: 0.5525 (t80) REVERT: M 249 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7922 (mm-30) REVERT: M 355 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6486 (tptm) REVERT: M 358 PHE cc_start: 0.7307 (m-10) cc_final: 0.6880 (m-10) REVERT: M 382 ASN cc_start: 0.7763 (m-40) cc_final: 0.7492 (m-40) REVERT: M 384 VAL cc_start: 0.8484 (t) cc_final: 0.7682 (m) REVERT: M 386 VAL cc_start: 0.8213 (t) cc_final: 0.7958 (m) REVERT: M 435 MET cc_start: 0.7503 (tmm) cc_final: 0.6529 (tmm) REVERT: M 481 ARG cc_start: 0.6261 (ttt180) cc_final: 0.5859 (ttt-90) REVERT: N 181 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5778 (p90) REVERT: N 321 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7638 (t80) REVERT: N 374 ARG cc_start: 0.7812 (ptt90) cc_final: 0.7450 (ptm-80) REVERT: N 409 LYS cc_start: 0.6531 (mttt) cc_final: 0.6283 (mmtp) REVERT: N 414 MET cc_start: 0.6661 (mmm) cc_final: 0.6071 (mmm) outliers start: 148 outliers final: 97 residues processed: 713 average time/residue: 0.2155 time to fit residues: 247.0689 Evaluate side-chains 708 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 591 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 368 TRP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 303 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 0.0000 chunk 336 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 329 optimal weight: 0.0670 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN I 89 GLN I 122 ASN I 302 GLN ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS J 270 ASN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.187394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.155129 restraints weight = 69825.671| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 4.32 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35032 Z= 0.126 Angle : 0.649 15.989 48160 Z= 0.336 Chirality : 0.043 0.386 5276 Planarity : 0.005 0.095 5488 Dihedral : 18.568 88.368 6388 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.24 % Allowed : 32.74 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3636 helix: 0.08 (0.14), residues: 1282 sheet: -1.24 (0.23), residues: 504 loop : -1.64 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 374 TYR 0.031 0.001 TYR E 37 PHE 0.031 0.001 PHE F 411 TRP 0.029 0.001 TRP J 369 HIS 0.009 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00289 (35032) covalent geometry : angle 0.64913 (48160) hydrogen bonds : bond 0.03448 ( 1128) hydrogen bonds : angle 5.07979 ( 3145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 608 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8178 (mttt) cc_final: 0.7780 (mttp) REVERT: A 89 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 100 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6437 (pt0) REVERT: A 251 HIS cc_start: 0.5477 (OUTLIER) cc_final: 0.5103 (m90) REVERT: A 262 TYR cc_start: 0.8241 (t80) cc_final: 0.7634 (t80) REVERT: A 303 MET cc_start: 0.6866 (tmm) cc_final: 0.6400 (tmm) REVERT: A 435 MET cc_start: 0.7962 (tpp) cc_final: 0.7682 (tpp) REVERT: B 14 ASP cc_start: 0.8640 (t0) cc_final: 0.8156 (t0) REVERT: B 105 TYR cc_start: 0.7151 (t80) cc_final: 0.6848 (t80) REVERT: B 171 TYR cc_start: 0.6931 (m-80) cc_final: 0.6663 (m-80) REVERT: B 219 TRP cc_start: 0.6707 (m100) cc_final: 0.5933 (m100) REVERT: B 279 ASP cc_start: 0.8197 (m-30) cc_final: 0.7709 (m-30) REVERT: B 283 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7549 (mmm160) REVERT: B 352 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8622 (mmtm) REVERT: B 361 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6942 (ttm110) REVERT: E 25 ASP cc_start: 0.7508 (m-30) cc_final: 0.7252 (m-30) REVERT: E 85 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7290 (pttm) REVERT: E 117 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6337 (mp) REVERT: E 205 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6606 (tm-30) REVERT: E 227 SER cc_start: 0.6341 (p) cc_final: 0.5996 (p) REVERT: E 336 LYS cc_start: 0.8573 (pttm) cc_final: 0.8370 (ptpp) REVERT: E 364 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5700 (mtm-85) REVERT: E 369 GLU cc_start: 0.8106 (pt0) cc_final: 0.7865 (pt0) REVERT: E 447 LYS cc_start: 0.7207 (mtpt) cc_final: 0.6959 (mtpt) REVERT: E 503 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.4526 (t80) REVERT: F 13 GLU cc_start: 0.7366 (mp0) cc_final: 0.6861 (mp0) REVERT: F 72 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5304 (tm-30) REVERT: F 122 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7886 (pttp) REVERT: F 135 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5008 (t80) REVERT: F 169 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6371 (mm-30) REVERT: F 324 SER cc_start: 0.8253 (t) cc_final: 0.7703 (p) REVERT: I 35 GLN cc_start: 0.6519 (tp40) cc_final: 0.6046 (tp40) REVERT: I 85 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.7000 (ptmm) REVERT: I 219 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6836 (pt) REVERT: I 302 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5756 (mp10) REVERT: I 368 GLU cc_start: 0.8315 (pp20) cc_final: 0.8024 (pp20) REVERT: I 400 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6213 (pm20) REVERT: I 444 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7262 (tm-30) REVERT: I 476 GLU cc_start: 0.7477 (pm20) cc_final: 0.7121 (pm20) REVERT: I 488 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: J 13 GLU cc_start: 0.8126 (mp0) cc_final: 0.7727 (mp0) REVERT: J 86 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8669 (mtpt) REVERT: J 130 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6286 (p0) REVERT: J 181 PHE cc_start: 0.8448 (t80) cc_final: 0.8030 (t80) REVERT: J 211 LYS cc_start: 0.6654 (mttt) cc_final: 0.5827 (mmmt) REVERT: J 219 TRP cc_start: 0.6674 (m-90) cc_final: 0.5920 (m-90) REVERT: J 271 LYS cc_start: 0.9167 (tptt) cc_final: 0.8848 (tptt) REVERT: J 277 MET cc_start: 0.7670 (mmm) cc_final: 0.7325 (mmm) REVERT: J 362 ARG cc_start: 0.3375 (OUTLIER) cc_final: 0.2363 (mmp-170) REVERT: M 97 THR cc_start: 0.8594 (p) cc_final: 0.8332 (t) REVERT: M 102 ARG cc_start: 0.8293 (tpm170) cc_final: 0.8085 (tpm170) REVERT: M 106 PHE cc_start: 0.0928 (OUTLIER) cc_final: -0.0033 (m-80) REVERT: M 150 TYR cc_start: 0.5822 (t80) cc_final: 0.5480 (t80) REVERT: M 249 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7857 (mp0) REVERT: M 355 LYS cc_start: 0.6956 (mtmt) cc_final: 0.6493 (tptm) REVERT: M 358 PHE cc_start: 0.7311 (m-10) cc_final: 0.6873 (m-10) REVERT: M 382 ASN cc_start: 0.7760 (m-40) cc_final: 0.7507 (m-40) REVERT: M 384 VAL cc_start: 0.8471 (t) cc_final: 0.7740 (m) REVERT: M 386 VAL cc_start: 0.8188 (t) cc_final: 0.7922 (m) REVERT: M 435 MET cc_start: 0.7500 (tmm) cc_final: 0.6544 (tmm) REVERT: M 481 ARG cc_start: 0.6211 (ttt180) cc_final: 0.5786 (ttt-90) REVERT: N 181 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.5756 (p90) REVERT: N 321 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7613 (t80) REVERT: N 374 ARG cc_start: 0.7916 (ptt90) cc_final: 0.7509 (ptm-80) REVERT: N 409 LYS cc_start: 0.6491 (mttt) cc_final: 0.6214 (mmtp) REVERT: N 414 MET cc_start: 0.6384 (mmm) cc_final: 0.5824 (mmm) outliers start: 139 outliers final: 91 residues processed: 694 average time/residue: 0.2090 time to fit residues: 232.6686 Evaluate side-chains 694 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 582 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 302 GLN Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 400 LYS Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 45 PHE Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 368 TRP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 321 optimal weight: 1.9990 chunk 110 optimal weight: 0.0020 chunk 61 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 332 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 122 ASN I 251 HIS I 302 GLN ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.185321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.152997 restraints weight = 69673.052| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 4.30 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35032 Z= 0.139 Angle : 0.674 15.286 48160 Z= 0.346 Chirality : 0.044 0.451 5276 Planarity : 0.005 0.077 5488 Dihedral : 18.576 87.766 6388 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.15 % Allowed : 32.99 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3636 helix: 0.12 (0.14), residues: 1274 sheet: -1.45 (0.22), residues: 520 loop : -1.59 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 24 TYR 0.035 0.001 TYR I 321 PHE 0.044 0.001 PHE M 503 TRP 0.050 0.002 TRP E 231 HIS 0.010 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00322 (35032) covalent geometry : angle 0.67371 (48160) hydrogen bonds : bond 0.03568 ( 1128) hydrogen bonds : angle 5.08456 ( 3145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 595 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8191 (mttt) cc_final: 0.7798 (mttp) REVERT: A 89 GLN cc_start: 0.7828 (pp30) cc_final: 0.7534 (pm20) REVERT: A 251 HIS cc_start: 0.5523 (OUTLIER) cc_final: 0.5175 (m90) REVERT: A 262 TYR cc_start: 0.8247 (t80) cc_final: 0.7758 (t80) REVERT: A 303 MET cc_start: 0.6914 (tmm) cc_final: 0.6423 (tmm) REVERT: A 406 MET cc_start: 0.7142 (tmm) cc_final: 0.6868 (tmm) REVERT: B 14 ASP cc_start: 0.8737 (t0) cc_final: 0.8266 (t0) REVERT: B 171 TYR cc_start: 0.6985 (m-80) cc_final: 0.6673 (m-80) REVERT: B 219 TRP cc_start: 0.6711 (m100) cc_final: 0.5939 (m100) REVERT: B 279 ASP cc_start: 0.8200 (m-30) cc_final: 0.7715 (m-30) REVERT: B 283 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7535 (mmm160) REVERT: B 352 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8643 (mmtm) REVERT: E 25 ASP cc_start: 0.7517 (m-30) cc_final: 0.7284 (m-30) REVERT: E 85 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7328 (pttm) REVERT: E 227 SER cc_start: 0.6465 (p) cc_final: 0.6099 (p) REVERT: E 295 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: E 364 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.5791 (mtm-85) REVERT: E 403 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6708 (t80) REVERT: E 476 GLU cc_start: 0.7247 (pm20) cc_final: 0.6827 (pm20) REVERT: E 503 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4463 (t80) REVERT: F 1 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (ptp) REVERT: F 13 GLU cc_start: 0.7413 (mp0) cc_final: 0.6928 (mp0) REVERT: F 72 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5420 (tm-30) REVERT: F 122 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7933 (pttp) REVERT: F 135 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5152 (t80) REVERT: F 169 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6376 (mm-30) REVERT: F 324 SER cc_start: 0.8268 (t) cc_final: 0.7709 (p) REVERT: I 8 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: I 35 GLN cc_start: 0.6561 (tp40) cc_final: 0.6084 (tp40) REVERT: I 85 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6955 (pptt) REVERT: I 132 ASP cc_start: 0.6426 (t0) cc_final: 0.6023 (m-30) REVERT: I 209 GLN cc_start: 0.7088 (tt0) cc_final: 0.6837 (tp40) REVERT: I 219 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6821 (pt) REVERT: I 302 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5637 (mp10) REVERT: I 368 GLU cc_start: 0.8332 (pp20) cc_final: 0.8021 (pp20) REVERT: I 400 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6300 (pm20) REVERT: I 444 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7223 (tm-30) REVERT: I 476 GLU cc_start: 0.7437 (pm20) cc_final: 0.6938 (pm20) REVERT: I 488 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: J 13 GLU cc_start: 0.8128 (mp0) cc_final: 0.7723 (mp0) REVERT: J 86 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8602 (mtpt) REVERT: J 171 TYR cc_start: 0.7858 (m-80) cc_final: 0.7578 (m-80) REVERT: J 181 PHE cc_start: 0.8525 (t80) cc_final: 0.8088 (t80) REVERT: J 211 LYS cc_start: 0.6589 (mttt) cc_final: 0.5782 (mmmt) REVERT: J 219 TRP cc_start: 0.6735 (m-90) cc_final: 0.6044 (m-90) REVERT: J 271 LYS cc_start: 0.9164 (mptt) cc_final: 0.8843 (tptt) REVERT: J 362 ARG cc_start: 0.3302 (OUTLIER) cc_final: 0.2386 (mmp-170) REVERT: J 364 GLN cc_start: 0.3699 (mm110) cc_final: 0.3483 (mm-40) REVERT: M 97 THR cc_start: 0.8606 (p) cc_final: 0.8351 (t) REVERT: M 102 ARG cc_start: 0.8419 (tpm170) cc_final: 0.8194 (tpm170) REVERT: M 106 PHE cc_start: 0.1035 (OUTLIER) cc_final: 0.0170 (m-80) REVERT: M 146 GLU cc_start: 0.7336 (mp0) cc_final: 0.6993 (mp0) REVERT: M 150 TYR cc_start: 0.6395 (t80) cc_final: 0.6120 (t80) REVERT: M 249 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7889 (mp0) REVERT: M 355 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6622 (tptm) REVERT: M 358 PHE cc_start: 0.7285 (m-10) cc_final: 0.6861 (m-10) REVERT: M 382 ASN cc_start: 0.7827 (m-40) cc_final: 0.7586 (m-40) REVERT: M 384 VAL cc_start: 0.8467 (t) cc_final: 0.7739 (m) REVERT: M 386 VAL cc_start: 0.8196 (t) cc_final: 0.7958 (m) REVERT: M 435 MET cc_start: 0.7596 (tmm) cc_final: 0.6597 (tmm) REVERT: M 481 ARG cc_start: 0.6280 (ttt180) cc_final: 0.5872 (ttt-90) REVERT: N 181 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.5500 (p90) REVERT: N 287 MET cc_start: 0.6180 (tpt) cc_final: 0.5410 (tpt) REVERT: N 321 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7623 (t80) REVERT: N 374 ARG cc_start: 0.7883 (ptt90) cc_final: 0.7653 (ptt90) REVERT: N 409 LYS cc_start: 0.6518 (mttt) cc_final: 0.6242 (mmtp) REVERT: N 414 MET cc_start: 0.6540 (mmm) cc_final: 0.5898 (mmm) outliers start: 136 outliers final: 98 residues processed: 678 average time/residue: 0.2080 time to fit residues: 226.3950 Evaluate side-chains 700 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 582 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 403 PHE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 302 GLN Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 400 LYS Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 433 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 368 TRP Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 183 optimal weight: 0.4980 chunk 267 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 253 optimal weight: 0.3980 chunk 55 optimal weight: 0.0370 chunk 213 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 297 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** J 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 122 ASN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.185071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.152749 restraints weight = 70227.196| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 4.34 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35032 Z= 0.140 Angle : 0.698 16.392 48160 Z= 0.356 Chirality : 0.044 0.439 5276 Planarity : 0.005 0.070 5488 Dihedral : 18.579 88.248 6388 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.02 % Allowed : 33.05 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3636 helix: 0.12 (0.14), residues: 1270 sheet: -1.41 (0.22), residues: 520 loop : -1.59 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG M 24 TYR 0.034 0.001 TYR I 321 PHE 0.043 0.001 PHE M 503 TRP 0.045 0.002 TRP E 231 HIS 0.010 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00325 (35032) covalent geometry : angle 0.69813 (48160) hydrogen bonds : bond 0.03572 ( 1128) hydrogen bonds : angle 5.10415 ( 3145) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 599 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1826 (tpp) cc_final: 0.1234 (tpt) REVERT: A 19 LYS cc_start: 0.8198 (mttt) cc_final: 0.7806 (mttp) REVERT: A 89 GLN cc_start: 0.7897 (pp30) cc_final: 0.7613 (pm20) REVERT: A 262 TYR cc_start: 0.8252 (t80) cc_final: 0.7759 (t80) REVERT: A 303 MET cc_start: 0.6878 (tmm) cc_final: 0.6427 (tmm) REVERT: A 356 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 406 MET cc_start: 0.7152 (tmm) cc_final: 0.6861 (tmm) REVERT: A 423 LEU cc_start: 0.7927 (mm) cc_final: 0.7543 (mt) REVERT: B 14 ASP cc_start: 0.8746 (t0) cc_final: 0.8274 (t0) REVERT: B 171 TYR cc_start: 0.6945 (m-80) cc_final: 0.6633 (m-80) REVERT: B 219 TRP cc_start: 0.6701 (m100) cc_final: 0.5980 (m100) REVERT: B 279 ASP cc_start: 0.8201 (m-30) cc_final: 0.7711 (m-30) REVERT: B 302 LYS cc_start: 0.8452 (tptp) cc_final: 0.7869 (mtmm) REVERT: B 352 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8634 (mmtm) REVERT: B 361 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7041 (ttm110) REVERT: E 25 ASP cc_start: 0.7550 (m-30) cc_final: 0.7304 (m-30) REVERT: E 72 ARG cc_start: 0.6369 (mpp80) cc_final: 0.5912 (mmm160) REVERT: E 85 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7360 (pttm) REVERT: E 227 SER cc_start: 0.6675 (p) cc_final: 0.6277 (p) REVERT: E 364 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.5671 (mtm-85) REVERT: E 403 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6679 (t80) REVERT: E 476 GLU cc_start: 0.7236 (pm20) cc_final: 0.6819 (pm20) REVERT: E 503 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.4450 (t80) REVERT: F 1 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8045 (ptp) REVERT: F 13 GLU cc_start: 0.7443 (mp0) cc_final: 0.6930 (mp0) REVERT: F 122 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7995 (pttp) REVERT: F 135 PHE cc_start: 0.5744 (OUTLIER) cc_final: 0.4697 (t80) REVERT: F 169 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6388 (mm-30) REVERT: F 277 MET cc_start: 0.8007 (tmm) cc_final: 0.7604 (tpt) REVERT: F 304 LYS cc_start: 0.8812 (tppt) cc_final: 0.8385 (tppt) REVERT: F 324 SER cc_start: 0.8281 (t) cc_final: 0.7723 (p) REVERT: I 8 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: I 35 GLN cc_start: 0.6568 (tp40) cc_final: 0.6117 (tp40) REVERT: I 85 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6986 (pptt) REVERT: I 209 GLN cc_start: 0.7135 (tt0) cc_final: 0.6887 (tp40) REVERT: I 219 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6806 (pt) REVERT: I 368 GLU cc_start: 0.8311 (pp20) cc_final: 0.8063 (pp20) REVERT: I 400 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6236 (pm20) REVERT: I 444 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7226 (tm-30) REVERT: I 476 GLU cc_start: 0.7403 (pm20) cc_final: 0.6960 (pm20) REVERT: I 488 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: I 497 LYS cc_start: 0.7986 (tppt) cc_final: 0.7781 (tppt) REVERT: J 13 GLU cc_start: 0.8098 (mp0) cc_final: 0.7701 (mp0) REVERT: J 86 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8639 (mtpt) REVERT: J 92 MET cc_start: 0.7228 (mtp) cc_final: 0.6976 (mtp) REVERT: J 126 LYS cc_start: 0.8700 (pttm) cc_final: 0.8494 (tmmt) REVERT: J 171 TYR cc_start: 0.7926 (m-80) cc_final: 0.7721 (m-80) REVERT: J 181 PHE cc_start: 0.8527 (t80) cc_final: 0.8155 (t80) REVERT: J 211 LYS cc_start: 0.6584 (mttt) cc_final: 0.5768 (mmmt) REVERT: J 219 TRP cc_start: 0.6739 (m-90) cc_final: 0.6165 (m-90) REVERT: J 271 LYS cc_start: 0.9167 (mptt) cc_final: 0.8823 (tptt) REVERT: J 274 GLU cc_start: 0.8643 (pp20) cc_final: 0.8310 (pp20) REVERT: J 277 MET cc_start: 0.7692 (mmm) cc_final: 0.7347 (mmm) REVERT: J 362 ARG cc_start: 0.3260 (OUTLIER) cc_final: 0.2341 (mmp-170) REVERT: J 364 GLN cc_start: 0.3736 (mm110) cc_final: 0.3524 (mm-40) REVERT: M 97 THR cc_start: 0.8624 (p) cc_final: 0.8362 (t) REVERT: M 102 ARG cc_start: 0.8427 (tpm170) cc_final: 0.8186 (tpm170) REVERT: M 106 PHE cc_start: 0.0997 (OUTLIER) cc_final: 0.0184 (m-80) REVERT: M 122 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7660 (t0) REVERT: M 150 TYR cc_start: 0.6254 (t80) cc_final: 0.5979 (t80) REVERT: M 249 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7861 (mp0) REVERT: M 355 LYS cc_start: 0.7056 (mtmt) cc_final: 0.6637 (tptm) REVERT: M 358 PHE cc_start: 0.7311 (m-10) cc_final: 0.6877 (m-10) REVERT: M 382 ASN cc_start: 0.7891 (m-40) cc_final: 0.7638 (m-40) REVERT: M 384 VAL cc_start: 0.8451 (t) cc_final: 0.7800 (m) REVERT: M 386 VAL cc_start: 0.8170 (t) cc_final: 0.7964 (m) REVERT: M 435 MET cc_start: 0.7605 (tmm) cc_final: 0.6519 (tmm) REVERT: N 92 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7641 (tpp) REVERT: N 181 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.5603 (p90) REVERT: N 277 MET cc_start: 0.6050 (ttt) cc_final: 0.5712 (mmm) REVERT: N 287 MET cc_start: 0.6188 (tpt) cc_final: 0.5465 (tpt) REVERT: N 321 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7633 (t80) REVERT: N 409 LYS cc_start: 0.6552 (mttt) cc_final: 0.6260 (mmtp) REVERT: N 414 MET cc_start: 0.6447 (mmm) cc_final: 0.5852 (mmm) outliers start: 132 outliers final: 102 residues processed: 679 average time/residue: 0.2126 time to fit residues: 231.6673 Evaluate side-chains 701 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 580 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 403 PHE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 400 LYS Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 433 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 122 ASN Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 436 GLU Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 368 TRP Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 387 ASP Chi-restraints excluded: chain N residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 210 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 168 optimal weight: 0.0570 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 364 optimal weight: 5.9990 chunk 227 optimal weight: 0.5980 chunk 154 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 229 optimal weight: 0.4980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 358 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS F 267 GLN F 358 HIS I 122 ASN I 217 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.186516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.154136 restraints weight = 69460.823| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 4.37 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35032 Z= 0.132 Angle : 0.688 17.367 48160 Z= 0.351 Chirality : 0.044 0.439 5276 Planarity : 0.005 0.069 5488 Dihedral : 18.558 88.836 6388 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.72 % Allowed : 33.57 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3636 helix: 0.11 (0.14), residues: 1272 sheet: -1.28 (0.22), residues: 528 loop : -1.61 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG M 24 TYR 0.028 0.001 TYR I 321 PHE 0.032 0.001 PHE A 442 TRP 0.049 0.001 TRP E 231 HIS 0.010 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00305 (35032) covalent geometry : angle 0.68838 (48160) hydrogen bonds : bond 0.03525 ( 1128) hydrogen bonds : angle 5.08320 ( 3145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7450.24 seconds wall clock time: 129 minutes 18.75 seconds (7758.75 seconds total)