Starting phenix.real_space_refine on Sun Aug 9 07:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8it1_35703/08_2026/8it1_35703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it1_35703/08_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_35703/08_2026/8it1_35703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it1_35703/08_2026/8it1_35703.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8it1_35703/08_2026/8it1_35703.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8it1_35703/08_2026/8it1_35703.cif" model { file = "/net/cci-nas-00/data/ceres_data/8it1_35703/08_2026/8it1_35703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it1_35703/08_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Time building chain proxies: 6.56, per 1000 atoms: 0.19 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 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: 4.15 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: 7.61 Time building geometry restraints manager: 3.89 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=" C3' DT K 38 " pdb=" O3' DT K 38 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C4' DT C 45 " pdb=" C3' DT C 45 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.00e-02 1.00e+04 9.33e+00 bond pdb=" C3' DT O 38 " pdb=" O3' DT O 38 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.32e+00 bond pdb=" C3' DA O 39 " pdb=" O3' DA O 39 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.08e+00 bond pdb=" C4' DC O 34 " pdb=" C3' DC O 34 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.93e+00 ... (remaining 35027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 47723 3.92 - 7.84: 407 7.84 - 11.77: 26 11.77 - 15.69: 3 15.69 - 19.61: 1 Bond angle restraints: 48160 Sorted by residual: angle pdb=" O4' DA O 29 " pdb=" C4' DA O 29 " pdb=" C3' DA O 29 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 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=" O4' DA G 29 " pdb=" C4' DA G 29 " pdb=" C3' DA G 29 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.88e+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=" O4' DT G 26 " pdb=" C1' DT G 26 " pdb=" N1 DT G 26 " ideal model delta sigma weight residual 108.00 111.46 -3.46 7.00e-01 2.04e+00 2.44e+01 ... (remaining 48155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 16124 18.17 - 36.33: 2938 36.33 - 54.50: 1092 54.50 - 72.67: 402 72.67 - 90.84: 100 Dihedral angle restraints: 20656 sinusoidal: 9876 harmonic: 10780 Sorted by residual: dihedral pdb=" C4' U D 6 " pdb=" C3' U D 6 " pdb=" C2' U D 6 " pdb=" C1' U D 6 " ideal model delta sinusoidal sigma weight residual 36.35 -42.50 78.85 1 3.10e+00 1.04e-01 8.06e+02 dihedral pdb=" C4' U L 6 " pdb=" C3' U L 6 " pdb=" C2' U L 6 " pdb=" C1' U L 6 " ideal model delta sinusoidal sigma weight residual 36.34 -42.39 78.73 1 3.10e+00 1.04e-01 8.04e+02 dihedral pdb=" C4' A L 3 " pdb=" C3' A L 3 " pdb=" C2' A L 3 " pdb=" C1' A L 3 " ideal model delta sinusoidal sigma weight residual 36.34 -41.99 78.34 1 3.10e+00 1.04e-01 7.97e+02 ... (remaining 20653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4495 0.080 - 0.160: 512 0.160 - 0.240: 105 0.240 - 0.320: 139 0.320 - 0.400: 25 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=" C3' G P 2 " pdb=" C4' G P 2 " pdb=" O3' G P 2 " pdb=" C2' G P 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.87 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C3' A L 3 " pdb=" C4' A L 3 " pdb=" O3' A L 3 " pdb=" C2' A L 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.86 0.36 2.00e-01 2.50e+01 3.30e+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: 0.02 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: 6.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.340 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 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= 0.301 Angle : 0.864 19.610 48160 Z= 0.478 Chirality : 0.075 0.400 5276 Planarity : 0.006 0.106 5488 Dihedral : 22.461 90.836 13688 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/Z covalent geometry : bond 0.00517 / 0.30 (35032) covalent geometry : angle 0.86392 / 0.48 (48160) hydrogen bonds : bond 0.19052 / 12.77 ( 1128) hydrogen bonds : angle 7.74851 / 5.46 ( 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 : 1.096 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: 0.2159 time to fit residues: 263.1325 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 : 0.980 ------------------------------------------------------------------------------- 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... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 466 ASN B 349 ASN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 122 ASN E 374 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS I 111 HIS ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN M 35 GLN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 454 GLN N 69 ASN N 234 ASN N 258 ASN N 320 HIS ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.195065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.162647 restraints weight = 70820.402| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 4.32 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 35032 Z= 0.257 Angle : 1.492 34.143 48160 Z= 0.627 Chirality : 0.144 1.576 5276 Planarity : 0.006 0.067 5488 Dihedral : 19.971 151.660 6069 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.75 % Allowed : 29.39 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.91 (0.13), residues: 3636 helix: -0.43 (0.14), residues: 1314 sheet: -1.46 (0.21), residues: 572 loop : -1.81 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 71 TYR 0.025 0.002 TYR F 221 PHE 0.020 0.002 PHE F 343 TRP 0.019 0.002 TRP F 369 HIS 0.012 0.001 HIS I 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.26 (35032) covalent geometry : angle 1.49248 / 0.63 (48160) hydrogen bonds : bond 0.04557 / 3.07 ( 1128) hydrogen bonds : angle 6.10969 / 4.24 ( 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 781 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 658 time to evaluate : 0.905 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 29 LEU cc_start: 0.8738 (tt) cc_final: 0.8537 (tt) REVERT: A 64 ILE cc_start: 0.6650 (tp) cc_final: 0.6357 (tp) REVERT: A 117 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 225 ARG cc_start: 0.7467 (ttm110) cc_final: 0.7103 (ttp-110) REVERT: A 251 HIS cc_start: 0.5579 (OUTLIER) cc_final: 0.5256 (m90) REVERT: A 262 TYR cc_start: 0.8166 (t80) cc_final: 0.7515 (t80) REVERT: A 279 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6828 (m) REVERT: A 305 LEU cc_start: 0.7685 (pp) cc_final: 0.7435 (tt) REVERT: A 383 LEU cc_start: 0.8340 (pt) cc_final: 0.8019 (pt) REVERT: A 458 ASP cc_start: 0.7362 (m-30) cc_final: 0.7115 (m-30) REVERT: B 14 ASP cc_start: 0.7716 (t0) cc_final: 0.7234 (t0) REVERT: B 16 ASP cc_start: 0.8266 (p0) cc_final: 0.8016 (p0) REVERT: B 37 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6986 (pp) REVERT: B 343 PHE cc_start: 0.7699 (m-80) cc_final: 0.7134 (m-10) REVERT: E 24 ARG cc_start: 0.6706 (mpp80) cc_final: 0.6336 (mtm180) REVERT: E 117 LEU cc_start: 0.7033 (tp) cc_final: 0.6768 (tt) REVERT: E 149 LYS cc_start: 0.6859 (tptt) cc_final: 0.6510 (tppt) REVERT: F 220 GLU cc_start: 0.7184 (mp0) cc_final: 0.6961 (mp0) REVERT: F 240 ARG cc_start: 0.7121 (mtm-85) cc_final: 0.6882 (mtm-85) REVERT: F 294 TRP cc_start: 0.6328 (p-90) cc_final: 0.5853 (p-90) REVERT: F 319 TRP cc_start: 0.7997 (p-90) cc_final: 0.7024 (p-90) REVERT: F 402 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7949 (pp) REVERT: I 118 VAL cc_start: 0.7803 (t) cc_final: 0.7514 (p) REVERT: I 474 ASP cc_start: 0.3678 (t0) cc_final: 0.2996 (t0) REVERT: J 138 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6943 (mp10) REVERT: J 181 PHE cc_start: 0.8271 (t80) cc_final: 0.8038 (t80) REVERT: J 271 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8778 (tptt) REVERT: J 274 GLU cc_start: 0.8277 (pp20) cc_final: 0.8070 (pp20) REVERT: J 433 ILE cc_start: 0.7127 (pt) cc_final: 0.6864 (mt) REVERT: M 1 MET cc_start: 0.5259 (ppp) cc_final: 0.5050 (ppp) REVERT: M 79 GLU cc_start: 0.7742 (pm20) cc_final: 0.7458 (mp0) REVERT: M 148 TYR cc_start: 0.7122 (t80) cc_final: 0.6888 (t80) REVERT: M 384 VAL cc_start: 0.8439 (t) cc_final: 0.7996 (m) REVERT: M 435 MET cc_start: 0.7129 (tmm) cc_final: 0.6734 (tmm) REVERT: M 481 ARG cc_start: 0.5985 (ttt180) cc_final: 0.5585 (ttt-90) REVERT: M 503 PHE cc_start: 0.5116 (t80) cc_final: 0.4893 (t80) REVERT: N 22 SER cc_start: 0.9092 (m) cc_final: 0.8834 (t) REVERT: N 158 PHE cc_start: 0.4631 (t80) cc_final: 0.4419 (t80) REVERT: N 318 TYR cc_start: 0.3320 (OUTLIER) cc_final: 0.3003 (m-80) outliers start: 123 outliers final: 51 residues processed: 731 average time/residue: 0.2033 time to fit residues: 237.6229 Evaluate side-chains 660 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 602 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 A residue 279 CYS 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 295 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 155 SER Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 283 LEU 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 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 217 PHE 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 261 CYS Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 361 ARG Chi-restraints excluded: chain F residue 395 VAL 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 489 ILE Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 271 LYS Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 96 ILE 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 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: 0.7980 chunk 329 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 353 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 151 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 90 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 270 ASN B 320 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN E 90 ASN E 129 ASN ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 HIS I 47 GLN I 111 HIS I 349 GLN ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 HIS N 69 ASN N 270 ASN ** 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 = 0.4760 r_free = 0.4760 target = 0.193586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.161186 restraints weight = 70454.254| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 4.37 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35032 Z= 0.187 Angle : 1.040 26.469 48160 Z= 0.459 Chirality : 0.092 1.355 5276 Planarity : 0.005 0.066 5488 Dihedral : 19.242 167.536 6068 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.93 % Allowed : 29.60 % Favored : 66.46 % 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: -1.79 (0.13), residues: 3636 helix: -0.27 (0.14), residues: 1297 sheet: -1.59 (0.22), residues: 488 loop : -1.74 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 283 TYR 0.024 0.001 TYR M 285 PHE 0.024 0.001 PHE F 205 TRP 0.024 0.002 TRP J 294 HIS 0.021 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (35032) covalent geometry : angle 1.04039 / 0.46 (48160) hydrogen bonds : bond 0.04767 / 3.15 ( 1128) hydrogen bonds : angle 5.71194 / 3.98 ( 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 752 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 623 time to evaluate : 1.227 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: A 29 LEU cc_start: 0.8846 (tt) cc_final: 0.8611 (tt) REVERT: A 64 ILE cc_start: 0.6618 (tp) cc_final: 0.6320 (tp) REVERT: A 117 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6871 (mt) REVERT: A 225 ARG cc_start: 0.7370 (ttm110) cc_final: 0.7138 (ttp-110) REVERT: A 262 TYR cc_start: 0.8153 (t80) cc_final: 0.7477 (t80) REVERT: A 383 LEU cc_start: 0.8370 (pt) cc_final: 0.8067 (pt) REVERT: A 406 MET cc_start: 0.6575 (tmm) cc_final: 0.6321 (tmm) REVERT: A 458 ASP cc_start: 0.7231 (m-30) cc_final: 0.6946 (m-30) REVERT: A 485 LYS cc_start: 0.6728 (tmtt) cc_final: 0.6464 (tmtt) REVERT: B 14 ASP cc_start: 0.7765 (t0) cc_final: 0.7187 (t0) REVERT: B 37 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6852 (pp) REVERT: B 101 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: B 275 LEU cc_start: 0.8360 (mt) cc_final: 0.8109 (mt) REVERT: B 304 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7866 (mmmt) REVERT: E 59 LYS cc_start: 0.7129 (mmmm) cc_final: 0.6746 (mttt) REVERT: E 331 LYS cc_start: 0.7976 (tptp) cc_final: 0.7735 (tppt) REVERT: E 353 TYR cc_start: 0.7606 (m-80) cc_final: 0.7383 (m-80) REVERT: E 409 ASN cc_start: 0.6826 (OUTLIER) cc_final: 0.6606 (p0) REVERT: E 444 GLU cc_start: 0.6182 (tm-30) cc_final: 0.5880 (tm-30) REVERT: F 52 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6425 (mt-10) REVERT: F 89 GLN cc_start: 0.7436 (pm20) cc_final: 0.7200 (pm20) REVERT: F 119 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7811 (p0) REVERT: F 135 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.5314 (t80) REVERT: F 147 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8363 (p-80) REVERT: F 277 MET cc_start: 0.8088 (tmm) cc_final: 0.7872 (tmm) REVERT: F 289 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7833 (mmtp) REVERT: F 294 TRP cc_start: 0.6362 (p-90) cc_final: 0.5624 (p-90) REVERT: F 304 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8650 (tppt) REVERT: F 336 MET cc_start: 0.5599 (mpp) cc_final: 0.5286 (mpp) REVERT: F 402 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7881 (pp) REVERT: F 406 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8119 (mmmt) REVERT: I 118 VAL cc_start: 0.7724 (t) cc_final: 0.7474 (p) REVERT: I 397 TYR cc_start: 0.5668 (m-10) cc_final: 0.5401 (m-10) REVERT: I 474 ASP cc_start: 0.3885 (t0) cc_final: 0.3638 (t0) REVERT: I 488 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: J 86 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8678 (mtpt) REVERT: J 181 PHE cc_start: 0.8388 (t80) cc_final: 0.8055 (t80) REVERT: J 219 TRP cc_start: 0.5540 (m-90) cc_final: 0.4959 (m-90) REVERT: J 233 TYR cc_start: 0.6605 (t80) cc_final: 0.6264 (t80) REVERT: J 270 ASN cc_start: 0.9164 (t0) cc_final: 0.8947 (t0) REVERT: J 271 LYS cc_start: 0.9229 (tptt) cc_final: 0.8880 (tptt) REVERT: J 293 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.5854 (m-80) REVERT: J 433 ILE cc_start: 0.7033 (pt) cc_final: 0.6808 (mt) REVERT: M 1 MET cc_start: 0.5368 (ppp) cc_final: 0.5094 (ppp) REVERT: M 79 GLU cc_start: 0.7826 (pm20) cc_final: 0.7596 (mp0) REVERT: M 106 PHE cc_start: 0.0981 (OUTLIER) cc_final: 0.0698 (m-80) REVERT: M 148 TYR cc_start: 0.7244 (t80) cc_final: 0.6963 (t80) REVERT: M 384 VAL cc_start: 0.8419 (t) cc_final: 0.7897 (m) REVERT: M 386 VAL cc_start: 0.7871 (t) cc_final: 0.7408 (m) REVERT: M 436 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6530 (mp0) REVERT: M 481 ARG cc_start: 0.6190 (ttt180) cc_final: 0.5876 (ttt-90) REVERT: M 503 PHE cc_start: 0.5212 (t80) cc_final: 0.4891 (t80) REVERT: N 22 SER cc_start: 0.9114 (m) cc_final: 0.8840 (t) REVERT: N 118 ILE cc_start: 0.9001 (tt) cc_final: 0.8797 (tt) REVERT: N 158 PHE cc_start: 0.4628 (t80) cc_final: 0.4254 (t80) REVERT: N 374 ARG cc_start: 0.7549 (ptm-80) cc_final: 0.7298 (ptm-80) outliers start: 129 outliers final: 63 residues processed: 696 average time/residue: 0.2216 time to fit residues: 246.5444 Evaluate side-chains 661 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 586 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 251 HIS 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 507 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 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 389 THR Chi-restraints excluded: chain E residue 409 ASN Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 493 SER 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 147 HIS Chi-restraints excluded: chain F residue 153 LEU 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 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 361 ARG Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE 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 437 VAL 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 62 ILE Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 287 MET Chi-restraints excluded: chain J residue 293 TYR 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 362 ARG Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE 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 443 ILE 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 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 163 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 90 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 374 ASN ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN M 251 HIS ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 466 ASN N 69 ASN N 258 ASN N 349 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.185804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.153414 restraints weight = 69770.827| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 4.25 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35032 Z= 0.224 Angle : 0.918 21.861 48160 Z= 0.431 Chirality : 0.075 1.012 5276 Planarity : 0.005 0.064 5488 Dihedral : 19.418 172.394 6068 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.27 % Allowed : 29.51 % Favored : 65.21 % 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: -1.76 (0.13), residues: 3636 helix: -0.14 (0.14), residues: 1279 sheet: -1.68 (0.22), residues: 486 loop : -1.76 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 24 TYR 0.024 0.002 TYR E 262 PHE 0.022 0.002 PHE A 419 TRP 0.040 0.002 TRP F 319 HIS 0.018 0.002 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (35032) covalent geometry : angle 0.91800 / 0.43 (48160) hydrogen bonds : bond 0.04688 / 3.04 ( 1128) hydrogen bonds : angle 5.55354 / 3.86 ( 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 809 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 636 time to evaluate : 0.952 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: 0.6641 (tp) cc_final: 0.6297 (tp) REVERT: A 100 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5548 (pt0) REVERT: A 117 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7134 (mt) REVERT: A 146 GLU cc_start: 0.7412 (pm20) cc_final: 0.6987 (tp30) REVERT: A 225 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7308 (ttp-110) REVERT: A 262 TYR cc_start: 0.8298 (t80) cc_final: 0.7886 (t80) REVERT: A 458 ASP cc_start: 0.7425 (m-30) cc_final: 0.7054 (m-30) REVERT: A 485 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6454 (tmtt) REVERT: B 14 ASP cc_start: 0.8377 (t0) cc_final: 0.7956 (t0) REVERT: B 16 ASP cc_start: 0.8474 (p0) cc_final: 0.8263 (p0) REVERT: B 159 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7461 (mp) REVERT: B 275 LEU cc_start: 0.8370 (mt) cc_final: 0.7861 (mp) REVERT: B 308 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5701 (tt) REVERT: B 352 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8491 (mmtm) REVERT: B 372 LYS cc_start: 0.8430 (tptp) cc_final: 0.8112 (tptt) REVERT: B 374 ARG cc_start: 0.4681 (ttp80) cc_final: 0.4367 (ttp80) REVERT: B 408 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6608 (tt) REVERT: E 59 LYS cc_start: 0.7125 (mmmm) cc_final: 0.6838 (mtmm) REVERT: E 74 MET cc_start: 0.6299 (pmm) cc_final: 0.6055 (pmm) REVERT: E 249 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7616 (mm-30) REVERT: E 444 GLU cc_start: 0.6262 (tm-30) cc_final: 0.5958 (tm-30) REVERT: F 13 GLU cc_start: 0.7315 (mp0) cc_final: 0.6792 (mp0) REVERT: F 89 GLN cc_start: 0.7999 (pm20) cc_final: 0.7597 (pm20) REVERT: F 119 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7761 (p0) REVERT: F 135 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5172 (t80) REVERT: F 147 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8678 (p-80) REVERT: F 220 GLU cc_start: 0.7547 (mp0) cc_final: 0.7318 (mp0) REVERT: F 250 ARG cc_start: 0.8129 (tpm170) cc_final: 0.7615 (tpm170) REVERT: F 267 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8480 (tm-30) REVERT: F 277 MET cc_start: 0.8176 (tmm) cc_final: 0.7876 (tmm) REVERT: F 289 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8244 (mmtt) REVERT: F 294 TRP cc_start: 0.6393 (p-90) cc_final: 0.5584 (p-90) REVERT: F 373 TRP cc_start: 0.8069 (m100) cc_final: 0.7845 (m100) REVERT: F 402 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7956 (pp) REVERT: I 8 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: I 35 GLN cc_start: 0.6326 (tp40) cc_final: 0.5759 (tp40) REVERT: I 118 VAL cc_start: 0.7892 (t) cc_final: 0.7588 (p) REVERT: I 331 LYS cc_start: 0.7288 (tptp) cc_final: 0.6822 (pttm) REVERT: I 397 TYR cc_start: 0.5802 (m-10) cc_final: 0.5329 (m-10) REVERT: I 400 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6174 (pm20) REVERT: I 488 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: I 497 LYS cc_start: 0.8092 (tppt) cc_final: 0.7834 (tppt) REVERT: J 13 GLU cc_start: 0.8056 (mp0) cc_final: 0.7761 (mp0) REVERT: J 86 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8706 (mtpt) REVERT: J 159 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7652 (tt) REVERT: J 181 PHE cc_start: 0.8443 (t80) cc_final: 0.8091 (t80) REVERT: J 219 TRP cc_start: 0.5891 (m-90) cc_final: 0.5128 (m-90) REVERT: J 229 LYS cc_start: 0.7884 (pttt) cc_final: 0.7664 (pttt) REVERT: J 256 ILE cc_start: 0.6203 (OUTLIER) cc_final: 0.4743 (mt) REVERT: J 271 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8902 (tptt) REVERT: J 274 GLU cc_start: 0.8550 (pp20) cc_final: 0.8245 (pp20) REVERT: J 374 ARG cc_start: 0.7918 (ttt180) cc_final: 0.7545 (ttt180) REVERT: J 433 ILE cc_start: 0.7216 (pt) cc_final: 0.6845 (mt) REVERT: M 1 MET cc_start: 0.5602 (ppp) cc_final: 0.5258 (ppp) REVERT: M 46 THR cc_start: 0.7095 (OUTLIER) cc_final: 0.6873 (t) REVERT: M 52 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7610 (mm) REVERT: M 97 THR cc_start: 0.8480 (p) cc_final: 0.8227 (t) REVERT: M 106 PHE cc_start: 0.0875 (OUTLIER) cc_final: 0.0018 (m-80) REVERT: M 146 GLU cc_start: 0.7089 (mp0) cc_final: 0.6880 (mp0) REVERT: M 150 TYR cc_start: 0.5755 (t80) cc_final: 0.5411 (t80) REVERT: M 358 PHE cc_start: 0.7324 (m-10) cc_final: 0.6829 (m-10) REVERT: M 384 VAL cc_start: 0.8412 (t) cc_final: 0.7798 (m) REVERT: M 386 VAL cc_start: 0.8104 (t) cc_final: 0.7656 (m) REVERT: M 435 MET cc_start: 0.7368 (tmm) cc_final: 0.7096 (tmm) REVERT: N 2 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7140 (ptp-170) REVERT: N 22 SER cc_start: 0.9134 (m) cc_final: 0.8849 (t) REVERT: N 90 ASP cc_start: 0.7309 (t0) cc_final: 0.7017 (t70) REVERT: N 118 ILE cc_start: 0.9064 (tt) cc_final: 0.8852 (tt) REVERT: N 287 MET cc_start: 0.6141 (tpt) cc_final: 0.5800 (tpt) REVERT: N 293 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6061 (t80) REVERT: N 374 ARG cc_start: 0.7580 (ptm-80) cc_final: 0.7193 (ptm-80) REVERT: N 409 LYS cc_start: 0.6761 (mttt) cc_final: 0.6501 (mmtp) REVERT: N 414 MET cc_start: 0.6921 (mmm) cc_final: 0.6599 (mmm) outliers start: 173 outliers final: 97 residues processed: 734 average time/residue: 0.2202 time to fit residues: 260.2272 Evaluate side-chains 722 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 603 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 122 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 ASP 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 462 LEU 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 123 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 159 LEU 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 261 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 408 LEU 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 313 PHE 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 493 SER Chi-restraints excluded: chain F residue 1 MET 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 147 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 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 375 GLU Chi-restraints excluded: chain F residue 401 ILE 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 111 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 279 CYS Chi-restraints excluded: chain I residue 383 LEU 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 62 ILE Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 271 LYS Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 328 LYS 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 21 THR Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 307 ASN Chi-restraints excluded: chain M residue 351 LYS Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 494 THR Chi-restraints excluded: chain N residue 2 ARG 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 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 214 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 293 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 Chi-restraints excluded: chain N residue 349 ASN Chi-restraints excluded: chain N residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.1980 chunk 310 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 322 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 251 HIS E 409 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 446 ASN J 69 ASN J 188 HIS J 270 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN N 69 ASN N 258 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.186671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.154175 restraints weight = 70353.912| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 4.30 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35032 Z= 0.170 Angle : 0.839 19.362 48160 Z= 0.398 Chirality : 0.071 1.016 5276 Planarity : 0.005 0.073 5488 Dihedral : 19.373 173.754 6068 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.79 % Allowed : 30.76 % Favored : 64.45 % 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: -1.72 (0.13), residues: 3636 helix: -0.11 (0.14), residues: 1281 sheet: -1.65 (0.22), residues: 495 loop : -1.74 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 72 TYR 0.028 0.001 TYR M 285 PHE 0.035 0.002 PHE E 206 TRP 0.021 0.001 TRP E 320 HIS 0.008 0.001 HIS I 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (35032) covalent geometry : angle 0.83860 / 0.40 (48160) hydrogen bonds : bond 0.04290 / 2.77 ( 1128) hydrogen bonds : angle 5.46242 / 3.79 ( 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 775 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 618 time to evaluate : 1.117 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: A 64 ILE cc_start: 0.6581 (tp) cc_final: 0.6308 (tp) REVERT: A 74 MET cc_start: 0.4196 (ppp) cc_final: 0.3987 (ppp) REVERT: A 100 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6012 (pt0) REVERT: A 117 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7028 (mt) REVERT: A 225 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7273 (ttp-110) REVERT: A 262 TYR cc_start: 0.8297 (t80) cc_final: 0.7829 (t80) REVERT: A 406 MET cc_start: 0.6941 (tmm) cc_final: 0.6670 (tmm) REVERT: A 458 ASP cc_start: 0.7436 (m-30) cc_final: 0.7079 (m-30) REVERT: A 485 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6424 (tmtt) REVERT: B 14 ASP cc_start: 0.8420 (t0) cc_final: 0.7985 (t0) REVERT: B 262 GLN cc_start: 0.8666 (pt0) cc_final: 0.8445 (pm20) REVERT: B 275 LEU cc_start: 0.8137 (mt) cc_final: 0.7867 (mt) REVERT: B 343 PHE cc_start: 0.8081 (m-80) cc_final: 0.7813 (m-10) REVERT: B 366 LYS cc_start: 0.6850 (mtmt) cc_final: 0.6616 (mtmt) REVERT: B 374 ARG cc_start: 0.4511 (ttp80) cc_final: 0.4174 (ttp80) REVERT: B 408 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6422 (tt) REVERT: E 50 LEU cc_start: 0.7379 (mt) cc_final: 0.7136 (mt) REVERT: E 59 LYS cc_start: 0.7077 (mmmm) cc_final: 0.6804 (mtmm) REVERT: E 74 MET cc_start: 0.6105 (pmm) cc_final: 0.5822 (pmm) REVERT: E 135 ARG cc_start: 0.6161 (tpt90) cc_final: 0.5959 (tpt-90) REVERT: E 205 GLN cc_start: 0.7002 (tm-30) cc_final: 0.6630 (tm-30) REVERT: E 364 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.5659 (mtm-85) REVERT: E 444 GLU cc_start: 0.6412 (tm-30) cc_final: 0.6136 (tm-30) REVERT: F 13 GLU cc_start: 0.7330 (mp0) cc_final: 0.6799 (mp0) REVERT: F 89 GLN cc_start: 0.8043 (pm20) cc_final: 0.7627 (pm20) REVERT: F 119 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.7811 (p0) REVERT: F 135 PHE cc_start: 0.5632 (OUTLIER) cc_final: 0.5137 (t80) REVERT: F 220 GLU cc_start: 0.7502 (mp0) cc_final: 0.7266 (mp0) REVERT: F 240 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6899 (mpp80) REVERT: F 250 ARG cc_start: 0.8114 (tpm170) cc_final: 0.7610 (tpm170) REVERT: F 277 MET cc_start: 0.8166 (tmm) cc_final: 0.7823 (tmm) REVERT: F 294 TRP cc_start: 0.6330 (p-90) cc_final: 0.5518 (p-90) REVERT: F 304 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8499 (tppt) REVERT: F 402 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8035 (pp) REVERT: F 434 ASN cc_start: 0.5550 (OUTLIER) cc_final: 0.3635 (m-40) REVERT: I 8 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: I 35 GLN cc_start: 0.6297 (tp40) cc_final: 0.5908 (tp40) REVERT: I 118 VAL cc_start: 0.7861 (t) cc_final: 0.7512 (p) REVERT: I 368 GLU cc_start: 0.8266 (pp20) cc_final: 0.7685 (pp20) REVERT: I 397 TYR cc_start: 0.5598 (m-80) cc_final: 0.5213 (m-80) REVERT: I 400 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.6053 (pm20) REVERT: I 444 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7254 (tm-30) REVERT: I 446 ASN cc_start: 0.5727 (OUTLIER) cc_final: 0.5209 (m-40) REVERT: I 476 GLU cc_start: 0.7497 (pm20) cc_final: 0.7161 (pm20) REVERT: I 488 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: I 497 LYS cc_start: 0.8079 (tppt) cc_final: 0.7809 (tppt) REVERT: J 13 GLU cc_start: 0.8090 (mp0) cc_final: 0.7760 (mp0) REVERT: J 138 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6996 (mp-120) REVERT: J 159 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7685 (tt) REVERT: J 181 PHE cc_start: 0.8469 (t80) cc_final: 0.8116 (t80) REVERT: J 219 TRP cc_start: 0.5975 (m-90) cc_final: 0.5240 (m-90) REVERT: J 271 LYS cc_start: 0.9223 (tptt) cc_final: 0.8924 (tptt) REVERT: M 1 MET cc_start: 0.5585 (ppp) cc_final: 0.5302 (ppp) REVERT: M 97 THR cc_start: 0.8489 (p) cc_final: 0.8232 (t) REVERT: M 102 ARG cc_start: 0.8121 (tpm170) cc_final: 0.7869 (tpm170) REVERT: M 106 PHE cc_start: 0.0870 (OUTLIER) cc_final: -0.0046 (m-80) REVERT: M 146 GLU cc_start: 0.7148 (mp0) cc_final: 0.6893 (mp0) REVERT: M 150 TYR cc_start: 0.5728 (t80) cc_final: 0.5401 (t80) REVERT: M 358 PHE cc_start: 0.7257 (m-10) cc_final: 0.6810 (m-10) REVERT: M 384 VAL cc_start: 0.8492 (t) cc_final: 0.7778 (m) REVERT: M 386 VAL cc_start: 0.8116 (t) cc_final: 0.7696 (m) REVERT: M 435 MET cc_start: 0.7354 (tmm) cc_final: 0.6928 (tmm) REVERT: M 436 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6269 (mt-10) REVERT: N 22 SER cc_start: 0.9110 (m) cc_final: 0.8827 (t) REVERT: N 90 ASP cc_start: 0.7310 (t0) cc_final: 0.7016 (t70) REVERT: N 118 ILE cc_start: 0.9043 (tt) cc_final: 0.8822 (tt) REVERT: N 287 MET cc_start: 0.5987 (tpt) cc_final: 0.5451 (tpt) REVERT: N 293 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.6156 (t80) REVERT: N 374 ARG cc_start: 0.7592 (ptm-80) cc_final: 0.7232 (ptm-80) REVERT: N 414 MET cc_start: 0.6849 (mmm) cc_final: 0.6283 (mmm) outliers start: 157 outliers final: 100 residues processed: 701 average time/residue: 0.2149 time to fit residues: 242.2209 Evaluate side-chains 702 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 585 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE 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 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 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 445 ILE Chi-restraints excluded: chain A residue 460 LEU 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 140 VAL Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 261 CYS 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 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 408 LEU 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 221 THR Chi-restraints excluded: chain E residue 313 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 F residue 11 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 62 ILE 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 208 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 261 CYS 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 378 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 401 ILE 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 F residue 434 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 219 ILE 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 446 ASN 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 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR 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 401 ILE 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 96 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 307 ASN 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 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 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 115 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 232 THR Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 256 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 344 optimal weight: 0.0670 chunk 195 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 354 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS J 270 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.185702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.153291 restraints weight = 70506.805| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 4.33 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35032 Z= 0.161 Angle : 0.811 18.993 48160 Z= 0.385 Chirality : 0.067 0.976 5276 Planarity : 0.005 0.069 5488 Dihedral : 19.347 176.940 6068 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.88 % Allowed : 31.22 % Favored : 63.90 % 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: -1.60 (0.13), residues: 3636 helix: -0.02 (0.14), residues: 1280 sheet: -1.44 (0.22), residues: 512 loop : -1.69 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 24 TYR 0.023 0.001 TYR E 262 PHE 0.025 0.001 PHE A 442 TRP 0.019 0.001 TRP E 320 HIS 0.018 0.001 HIS I 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (35032) covalent geometry : angle 0.81064 / 0.39 (48160) hydrogen bonds : bond 0.04173 / 2.68 ( 1128) hydrogen bonds : angle 5.35563 / 3.72 ( 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 785 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 625 time to evaluate : 1.185 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 19 LYS cc_start: 0.8044 (mttt) cc_final: 0.7736 (mttp) REVERT: A 64 ILE cc_start: 0.6566 (tp) cc_final: 0.6312 (tp) REVERT: A 100 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5933 (pt0) REVERT: A 117 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7086 (mt) REVERT: A 225 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7388 (ttp-110) REVERT: A 262 TYR cc_start: 0.8271 (t80) cc_final: 0.7745 (t80) REVERT: A 406 MET cc_start: 0.6974 (tmm) cc_final: 0.6752 (tmm) REVERT: A 447 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7579 (mmtt) REVERT: A 458 ASP cc_start: 0.7453 (m-30) cc_final: 0.7098 (m-30) REVERT: A 485 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6333 (tmtt) REVERT: B 14 ASP cc_start: 0.8507 (t0) cc_final: 0.8136 (t0) REVERT: B 262 GLN cc_start: 0.8598 (pt0) cc_final: 0.8389 (pm20) REVERT: B 304 LYS cc_start: 0.8250 (mmmt) cc_final: 0.8014 (mmmt) REVERT: B 352 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8431 (mmtm) REVERT: B 366 LYS cc_start: 0.6873 (mtmt) cc_final: 0.6623 (mtmt) REVERT: B 374 ARG cc_start: 0.4695 (ttp80) cc_final: 0.4384 (ttp80) REVERT: B 408 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6542 (tt) REVERT: E 50 LEU cc_start: 0.7439 (mt) cc_final: 0.7136 (mt) REVERT: E 59 LYS cc_start: 0.7085 (mmmm) cc_final: 0.6870 (mtmm) REVERT: E 74 MET cc_start: 0.6046 (pmm) cc_final: 0.5714 (pmm) REVERT: E 364 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.5725 (mtm-85) REVERT: E 444 GLU cc_start: 0.6395 (tm-30) cc_final: 0.6183 (tm-30) REVERT: E 503 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4290 (t80) REVERT: F 13 GLU cc_start: 0.7329 (mp0) cc_final: 0.6768 (mp0) REVERT: F 89 GLN cc_start: 0.8111 (pm20) cc_final: 0.7746 (pm20) REVERT: F 119 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7901 (p0) REVERT: F 135 PHE cc_start: 0.5728 (OUTLIER) cc_final: 0.5151 (t80) REVERT: F 161 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.5379 (m-30) REVERT: F 220 GLU cc_start: 0.7430 (mp0) cc_final: 0.7187 (mp0) REVERT: F 240 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6948 (mpp80) REVERT: F 250 ARG cc_start: 0.8067 (tpm170) cc_final: 0.7544 (tpm170) REVERT: F 277 MET cc_start: 0.8048 (tmm) cc_final: 0.7676 (tmm) REVERT: F 289 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8346 (mmtt) REVERT: F 294 TRP cc_start: 0.6380 (p-90) cc_final: 0.5630 (p-90) REVERT: F 324 SER cc_start: 0.8120 (t) cc_final: 0.7615 (p) REVERT: F 336 MET cc_start: 0.6041 (mpp) cc_final: 0.5406 (mpp) REVERT: I 8 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: I 35 GLN cc_start: 0.6431 (tp40) cc_final: 0.6040 (tp40) REVERT: I 85 LYS cc_start: 0.7317 (pttt) cc_final: 0.6878 (pptt) REVERT: I 118 VAL cc_start: 0.7923 (t) cc_final: 0.7583 (p) REVERT: I 368 GLU cc_start: 0.8113 (pp20) cc_final: 0.7662 (pp20) REVERT: I 397 TYR cc_start: 0.5553 (m-80) cc_final: 0.5240 (m-80) REVERT: I 476 GLU cc_start: 0.7406 (pm20) cc_final: 0.7095 (pm20) REVERT: I 488 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: I 497 LYS cc_start: 0.8029 (tppt) cc_final: 0.7786 (tppt) REVERT: J 13 GLU cc_start: 0.8018 (mp0) cc_final: 0.7775 (mp0) REVERT: J 55 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6402 (mt-10) REVERT: J 138 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7161 (mp-120) REVERT: J 159 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7823 (tt) REVERT: J 181 PHE cc_start: 0.8425 (t80) cc_final: 0.8107 (t80) REVERT: J 211 LYS cc_start: 0.4638 (mttp) cc_final: 0.2741 (mmmt) REVERT: J 219 TRP cc_start: 0.6037 (m-90) cc_final: 0.5343 (m-90) REVERT: J 256 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5608 (mm) REVERT: J 271 LYS cc_start: 0.9137 (tptt) cc_final: 0.8790 (tptt) REVERT: J 277 MET cc_start: 0.7664 (mmm) cc_final: 0.7370 (mmm) REVERT: J 362 ARG cc_start: 0.3477 (OUTLIER) cc_final: 0.2702 (mmp-170) REVERT: J 401 ILE cc_start: 0.7963 (mm) cc_final: 0.7763 (tp) REVERT: M 1 MET cc_start: 0.5444 (ppp) cc_final: 0.5197 (ppp) REVERT: M 97 THR cc_start: 0.8531 (p) cc_final: 0.8263 (t) REVERT: M 102 ARG cc_start: 0.8201 (tpm170) cc_final: 0.7927 (tpm170) REVERT: M 106 PHE cc_start: 0.0883 (OUTLIER) cc_final: -0.0050 (m-80) REVERT: M 146 GLU cc_start: 0.7119 (mp0) cc_final: 0.6858 (mp0) REVERT: M 150 TYR cc_start: 0.5686 (t80) cc_final: 0.5369 (t80) REVERT: M 358 PHE cc_start: 0.7150 (m-10) cc_final: 0.6727 (m-10) REVERT: M 384 VAL cc_start: 0.8547 (t) cc_final: 0.7797 (m) REVERT: M 386 VAL cc_start: 0.8139 (t) cc_final: 0.7741 (m) REVERT: M 435 MET cc_start: 0.7454 (tmm) cc_final: 0.6906 (tmm) REVERT: M 436 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6396 (mt-10) REVERT: N 22 SER cc_start: 0.9123 (m) cc_final: 0.8855 (t) REVERT: N 90 ASP cc_start: 0.7272 (t0) cc_final: 0.7022 (t70) REVERT: N 152 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8248 (tp) REVERT: N 181 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.5775 (p90) REVERT: N 205 PHE cc_start: 0.7080 (t80) cc_final: 0.6868 (t80) REVERT: N 287 MET cc_start: 0.5921 (tpt) cc_final: 0.5385 (tpt) REVERT: N 293 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.6020 (t80) REVERT: N 374 ARG cc_start: 0.7635 (ptm-80) cc_final: 0.7287 (ptm-80) REVERT: N 414 MET cc_start: 0.6901 (mmm) cc_final: 0.6360 (mmm) outliers start: 160 outliers final: 105 residues processed: 712 average time/residue: 0.2207 time to fit residues: 252.3927 Evaluate side-chains 724 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 599 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 112 LYS 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 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 460 LEU Chi-restraints excluded: chain A residue 485 LYS 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 234 ASN 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 408 LEU 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 221 THR Chi-restraints excluded: chain E residue 313 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 406 MET Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 493 SER 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 58 CYS Chi-restraints excluded: chain F residue 62 ILE 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 161 ASP Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 261 CYS 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 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 111 HIS Chi-restraints excluded: chain I residue 219 ILE 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 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU 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 21 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 307 ASN 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 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 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 115 LEU Chi-restraints excluded: chain N residue 152 LEU 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 232 THR Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 6 optimal weight: 0.4980 chunk 292 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 342 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 365 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS J 270 ASN ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 454 GLN 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 = 0.4627 r_free = 0.4627 target = 0.181763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.149321 restraints weight = 71073.825| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 4.32 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35032 Z= 0.199 Angle : 0.839 19.356 48160 Z= 0.405 Chirality : 0.066 1.001 5276 Planarity : 0.005 0.070 5488 Dihedral : 19.380 178.695 6068 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.43 % Allowed : 31.19 % Favored : 63.38 % 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: -1.71 (0.13), residues: 3636 helix: -0.08 (0.14), residues: 1280 sheet: -1.55 (0.22), residues: 532 loop : -1.77 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 24 TYR 0.032 0.002 TYR E 285 PHE 0.029 0.002 PHE A 30 TRP 0.022 0.002 TRP E 320 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (35032) covalent geometry : angle 0.83904 / 0.41 (48160) hydrogen bonds : bond 0.04474 / 2.90 ( 1128) hydrogen bonds : angle 5.39960 / 3.74 ( 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 801 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 623 time to evaluate : 1.178 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 1 MET cc_start: 0.1835 (tpp) cc_final: 0.1122 (tpt) REVERT: A 19 LYS cc_start: 0.8047 (mttt) cc_final: 0.7686 (mttp) REVERT: A 64 ILE cc_start: 0.6559 (tp) cc_final: 0.6264 (tp) REVERT: A 100 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6084 (pt0) REVERT: A 225 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7408 (ttp-110) REVERT: A 262 TYR cc_start: 0.8387 (t80) cc_final: 0.8010 (t80) REVERT: A 435 MET cc_start: 0.7826 (tpp) cc_final: 0.7567 (tpp) REVERT: A 458 ASP cc_start: 0.7495 (m-30) cc_final: 0.7250 (m-30) REVERT: A 485 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.5988 (mmtt) REVERT: B 14 ASP cc_start: 0.8690 (t0) cc_final: 0.8295 (t0) REVERT: B 262 GLN cc_start: 0.8663 (pt0) cc_final: 0.8407 (pm20) REVERT: B 352 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8571 (mmtm) REVERT: E 50 LEU cc_start: 0.7387 (mt) cc_final: 0.7082 (mt) REVERT: E 59 LYS cc_start: 0.7071 (mmmm) cc_final: 0.6849 (mtmm) REVERT: E 364 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.5815 (mtm-85) REVERT: E 444 GLU cc_start: 0.6372 (tm-30) cc_final: 0.6160 (tm-30) REVERT: E 503 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.4197 (t80) REVERT: F 13 GLU cc_start: 0.7380 (mp0) cc_final: 0.6628 (mp0) REVERT: F 72 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5679 (tm-30) REVERT: F 89 GLN cc_start: 0.8273 (pm20) cc_final: 0.7857 (pm20) REVERT: F 111 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7588 (tp30) REVERT: F 119 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8013 (p0) REVERT: F 135 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5169 (t80) REVERT: F 161 ASP cc_start: 0.5534 (OUTLIER) cc_final: 0.5264 (m-30) REVERT: F 240 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6951 (mpp80) REVERT: F 250 ARG cc_start: 0.8100 (tpm170) cc_final: 0.7565 (tpm170) REVERT: F 277 MET cc_start: 0.8163 (tmm) cc_final: 0.7764 (tmm) REVERT: F 289 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8530 (mmtt) REVERT: F 294 TRP cc_start: 0.6358 (p-90) cc_final: 0.5595 (p-90) REVERT: F 324 SER cc_start: 0.8220 (t) cc_final: 0.7680 (p) REVERT: F 336 MET cc_start: 0.5930 (mpp) cc_final: 0.5404 (mpp) REVERT: I 8 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: I 35 GLN cc_start: 0.6579 (tp40) cc_final: 0.6199 (tp40) REVERT: I 59 LYS cc_start: 0.7177 (mtpp) cc_final: 0.6963 (mtmm) REVERT: I 118 VAL cc_start: 0.7950 (t) cc_final: 0.7628 (p) REVERT: I 368 GLU cc_start: 0.8287 (pp20) cc_final: 0.7839 (pp20) REVERT: I 397 TYR cc_start: 0.5669 (m-80) cc_final: 0.5248 (m-80) REVERT: I 474 ASP cc_start: 0.4262 (t0) cc_final: 0.3560 (t0) REVERT: I 488 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: I 497 LYS cc_start: 0.8158 (tppt) cc_final: 0.7884 (tppt) REVERT: J 13 GLU cc_start: 0.8083 (mp0) cc_final: 0.7765 (mp0) REVERT: J 55 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6464 (mt-10) REVERT: J 138 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7126 (mp-120) REVERT: J 159 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7790 (tt) REVERT: J 181 PHE cc_start: 0.8519 (t80) cc_final: 0.8159 (t80) REVERT: J 219 TRP cc_start: 0.6265 (m-90) cc_final: 0.5515 (m-90) REVERT: J 256 ILE cc_start: 0.6330 (mp) cc_final: 0.5059 (mt) REVERT: J 271 LYS cc_start: 0.9216 (tptt) cc_final: 0.8882 (tptt) REVERT: J 274 GLU cc_start: 0.8639 (pp20) cc_final: 0.8097 (pp20) REVERT: J 362 ARG cc_start: 0.3741 (OUTLIER) cc_final: 0.2865 (mmp-170) REVERT: J 401 ILE cc_start: 0.8006 (mm) cc_final: 0.7787 (tp) REVERT: J 445 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4812 (tm-30) REVERT: M 1 MET cc_start: 0.5599 (ppp) cc_final: 0.5366 (ppp) REVERT: M 46 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6442 (t) REVERT: M 97 THR cc_start: 0.8557 (p) cc_final: 0.8295 (t) REVERT: M 102 ARG cc_start: 0.8318 (tpm170) cc_final: 0.8101 (tpm170) REVERT: M 106 PHE cc_start: 0.0919 (OUTLIER) cc_final: 0.0165 (m-80) REVERT: M 150 TYR cc_start: 0.5824 (t80) cc_final: 0.5524 (t80) REVERT: M 358 PHE cc_start: 0.7343 (m-10) cc_final: 0.6902 (m-10) REVERT: M 384 VAL cc_start: 0.8531 (t) cc_final: 0.7716 (m) REVERT: M 386 VAL cc_start: 0.8253 (t) cc_final: 0.7813 (m) REVERT: M 435 MET cc_start: 0.7529 (tmm) cc_final: 0.6841 (tmm) REVERT: M 436 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6436 (mt-10) REVERT: N 118 ILE cc_start: 0.9079 (tt) cc_final: 0.8860 (tt) REVERT: N 152 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8315 (tp) REVERT: N 181 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5800 (p90) REVERT: N 192 TRP cc_start: 0.7316 (p-90) cc_final: 0.6933 (p-90) REVERT: N 293 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6068 (t80) REVERT: N 321 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7769 (t80) REVERT: N 409 LYS cc_start: 0.6732 (mttt) cc_final: 0.6473 (mmtp) REVERT: N 414 MET cc_start: 0.6870 (mmm) cc_final: 0.6313 (mmm) outliers start: 178 outliers final: 113 residues processed: 725 average time/residue: 0.2214 time to fit residues: 257.3355 Evaluate side-chains 733 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 599 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 112 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 285 TYR 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 460 LEU Chi-restraints excluded: chain A residue 485 LYS 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 261 CYS Chi-restraints excluded: chain B residue 265 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 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 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 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 119 ASP Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 147 HIS 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 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 261 CYS 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 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 84 CYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 111 HIS 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 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 118 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR 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 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 307 ASN 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 426 VAL 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 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 84 VAL 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 232 THR Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 321 PHE 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 429 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 303 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 336 optimal weight: 0.5980 chunk 314 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 329 optimal weight: 0.0170 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN A 90 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS I 302 GLN ** I 430 GLN ** 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** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.185522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.153170 restraints weight = 70132.454| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 4.33 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4131 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= 0.147 Angle : 0.816 19.552 48160 Z= 0.392 Chirality : 0.064 0.999 5276 Planarity : 0.005 0.106 5488 Dihedral : 19.336 178.490 6068 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.33 % Allowed : 32.47 % Favored : 63.20 % 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: 0.03 (0.14), residues: 1280 sheet: -1.42 (0.22), residues: 508 loop : -1.73 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 113 TYR 0.028 0.001 TYR M 285 PHE 0.047 0.001 PHE M 503 TRP 0.022 0.001 TRP I 421 HIS 0.008 0.001 HIS I 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (35032) covalent geometry : angle 0.81631 / 0.39 (48160) hydrogen bonds : bond 0.04090 / 2.59 ( 1128) hydrogen bonds : angle 5.29487 / 3.68 ( 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 748 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 606 time to evaluate : 1.128 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: 0.8034 (mttt) cc_final: 0.7598 (mttp) REVERT: A 64 ILE cc_start: 0.6386 (tp) cc_final: 0.6151 (tp) REVERT: A 225 ARG cc_start: 0.7621 (ttm110) cc_final: 0.7212 (ttp-110) REVERT: A 262 TYR cc_start: 0.8253 (t80) cc_final: 0.7748 (t80) REVERT: A 406 MET cc_start: 0.6943 (tmm) cc_final: 0.6680 (tmm) REVERT: A 458 ASP cc_start: 0.7446 (m-30) cc_final: 0.7208 (m-30) REVERT: A 485 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.5941 (mmtt) REVERT: B 14 ASP cc_start: 0.8568 (t0) cc_final: 0.8154 (t0) REVERT: B 219 TRP cc_start: 0.6494 (m100) cc_final: 0.5346 (m100) REVERT: B 343 PHE cc_start: 0.8251 (m-80) cc_final: 0.7939 (m-10) REVERT: B 352 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8605 (mmtm) REVERT: E 227 SER cc_start: 0.6417 (p) cc_final: 0.6084 (p) REVERT: E 286 LYS cc_start: 0.7660 (tptp) cc_final: 0.7377 (tppt) REVERT: E 364 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.5732 (mtm-85) REVERT: E 369 GLU cc_start: 0.8029 (pt0) cc_final: 0.7761 (pt0) REVERT: E 503 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.4401 (t80) REVERT: F 13 GLU cc_start: 0.7347 (mp0) cc_final: 0.6613 (mp0) REVERT: F 72 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5601 (tm-30) REVERT: F 89 GLN cc_start: 0.8137 (pm20) cc_final: 0.7804 (pm20) REVERT: F 111 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7479 (tp30) REVERT: F 119 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8036 (p0) REVERT: F 135 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.5040 (t80) REVERT: F 161 ASP cc_start: 0.5459 (OUTLIER) cc_final: 0.5170 (m-30) REVERT: F 240 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.7057 (mpp80) REVERT: F 250 ARG cc_start: 0.8022 (tpm170) cc_final: 0.7484 (tpm170) REVERT: F 277 MET cc_start: 0.7993 (tmm) cc_final: 0.7600 (tmm) REVERT: F 289 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8553 (mmtt) REVERT: F 324 SER cc_start: 0.8186 (t) cc_final: 0.7643 (p) REVERT: F 336 MET cc_start: 0.5861 (mpp) cc_final: 0.5352 (mpp) REVERT: I 35 GLN cc_start: 0.6561 (tp40) cc_final: 0.6128 (tp40) REVERT: I 118 VAL cc_start: 0.7872 (t) cc_final: 0.7528 (p) REVERT: I 368 GLU cc_start: 0.8062 (pp20) cc_final: 0.7834 (pp20) REVERT: I 397 TYR cc_start: 0.5423 (m-80) cc_final: 0.4970 (m-10) REVERT: I 420 LEU cc_start: 0.6727 (tp) cc_final: 0.6486 (tp) REVERT: I 488 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: I 497 LYS cc_start: 0.8097 (tppt) cc_final: 0.7845 (tppt) REVERT: J 13 GLU cc_start: 0.8013 (mp0) cc_final: 0.7726 (mp0) REVERT: J 138 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.7068 (mp-120) REVERT: J 181 PHE cc_start: 0.8467 (t80) cc_final: 0.8128 (t80) REVERT: J 219 TRP cc_start: 0.6225 (m-90) cc_final: 0.5503 (m-90) REVERT: J 271 LYS cc_start: 0.9140 (tptt) cc_final: 0.8743 (tptt) REVERT: J 277 MET cc_start: 0.7640 (mmm) cc_final: 0.7312 (mmm) REVERT: M 1 MET cc_start: 0.5559 (ppp) cc_final: 0.5341 (ppp) REVERT: M 52 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7706 (mm) REVERT: M 97 THR cc_start: 0.8567 (p) cc_final: 0.8300 (t) REVERT: M 102 ARG cc_start: 0.8360 (tpm170) cc_final: 0.8142 (tpm170) REVERT: M 106 PHE cc_start: 0.0885 (OUTLIER) cc_final: 0.0055 (m-80) REVERT: M 150 TYR cc_start: 0.5769 (t80) cc_final: 0.5472 (t80) REVERT: M 249 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7917 (mm-30) REVERT: M 358 PHE cc_start: 0.7286 (m-10) cc_final: 0.6877 (m-10) REVERT: M 384 VAL cc_start: 0.8553 (t) cc_final: 0.7734 (m) REVERT: M 386 VAL cc_start: 0.8174 (t) cc_final: 0.7749 (m) REVERT: M 435 MET cc_start: 0.7430 (tmm) cc_final: 0.6735 (tmm) REVERT: M 436 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6402 (mt-10) REVERT: M 481 ARG cc_start: 0.6269 (ttt180) cc_final: 0.6039 (ttt-90) REVERT: N 181 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.5723 (p90) REVERT: N 192 TRP cc_start: 0.7171 (p-90) cc_final: 0.6934 (p-90) REVERT: N 287 MET cc_start: 0.6442 (tpt) cc_final: 0.6115 (tpt) REVERT: N 321 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7707 (t80) REVERT: N 374 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.7392 (ptm-80) REVERT: N 409 LYS cc_start: 0.6631 (mttt) cc_final: 0.6342 (mmtp) REVERT: N 414 MET cc_start: 0.6799 (mmm) cc_final: 0.6251 (mmm) outliers start: 142 outliers final: 101 residues processed: 690 average time/residue: 0.2214 time to fit residues: 245.0232 Evaluate side-chains 699 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 584 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 ASP 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 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 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 140 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 265 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 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 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 62 ILE Chi-restraints excluded: chain F residue 72 GLU 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 147 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 ASP 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 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 13 LEU Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 283 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 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU 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 43 VAL Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE 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 426 VAL 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 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 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 293 TYR Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 321 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 286 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** I 430 GLN ** 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 35 GLN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 360 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.182068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.149729 restraints weight = 69926.196| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 4.28 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35032 Z= 0.184 Angle : 0.838 20.518 48160 Z= 0.404 Chirality : 0.064 1.020 5276 Planarity : 0.005 0.107 5488 Dihedral : 19.345 178.132 6068 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.30 % Allowed : 32.56 % Favored : 63.14 % 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: -1.68 (0.13), residues: 3636 helix: -0.04 (0.14), residues: 1280 sheet: -1.56 (0.22), residues: 528 loop : -1.76 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 113 TYR 0.028 0.002 TYR E 6 PHE 0.036 0.002 PHE A 30 TRP 0.051 0.002 TRP J 369 HIS 0.007 0.001 HIS I 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (35032) covalent geometry : angle 0.83803 / 0.40 (48160) hydrogen bonds : bond 0.04310 / 2.78 ( 1128) hydrogen bonds : angle 5.30758 / 3.68 ( 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 748 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 607 time to evaluate : 1.181 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: A 19 LYS cc_start: 0.8070 (mttt) cc_final: 0.7636 (mttp) REVERT: A 64 ILE cc_start: 0.6412 (tp) cc_final: 0.6171 (tp) REVERT: A 72 ARG cc_start: 0.6315 (mpp80) cc_final: 0.5601 (mpp80) REVERT: A 225 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7395 (ttp-110) REVERT: A 234 PHE cc_start: 0.6727 (m-10) cc_final: 0.6504 (m-10) REVERT: A 262 TYR cc_start: 0.8366 (t80) cc_final: 0.7901 (t80) REVERT: A 356 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 406 MET cc_start: 0.7181 (tmm) cc_final: 0.6903 (tmm) REVERT: A 435 MET cc_start: 0.7835 (tpp) cc_final: 0.7552 (tpp) REVERT: A 458 ASP cc_start: 0.7531 (m-30) cc_final: 0.7277 (m-30) REVERT: A 485 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.5930 (mmtt) REVERT: B 14 ASP cc_start: 0.8686 (t0) cc_final: 0.8304 (t0) REVERT: B 105 TYR cc_start: 0.7265 (t80) cc_final: 0.6939 (t80) REVERT: B 193 ARG cc_start: 0.6162 (ptt-90) cc_final: 0.5901 (ptp90) REVERT: B 219 TRP cc_start: 0.6640 (m100) cc_final: 0.5407 (m100) REVERT: B 262 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: B 283 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7339 (mmm160) REVERT: B 343 PHE cc_start: 0.8304 (m-80) cc_final: 0.7994 (m-10) REVERT: B 352 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8656 (mmtm) REVERT: E 135 ARG cc_start: 0.6277 (tpt90) cc_final: 0.5867 (tpt-90) REVERT: E 227 SER cc_start: 0.6481 (p) cc_final: 0.6148 (p) REVERT: E 364 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.5817 (mtm-85) REVERT: E 503 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.4361 (t80) REVERT: F 72 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5673 (tm-30) REVERT: F 89 GLN cc_start: 0.8272 (pm20) cc_final: 0.7883 (pm20) REVERT: F 111 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7642 (tp30) REVERT: F 135 PHE cc_start: 0.5854 (OUTLIER) cc_final: 0.5142 (t80) REVERT: F 157 ILE cc_start: 0.4874 (OUTLIER) cc_final: 0.4542 (tt) REVERT: F 240 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.7107 (mpp80) REVERT: F 277 MET cc_start: 0.8050 (tmm) cc_final: 0.7516 (tmm) REVERT: F 289 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8647 (mmtt) REVERT: F 304 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8466 (tppt) REVERT: F 324 SER cc_start: 0.8272 (t) cc_final: 0.7755 (p) REVERT: F 336 MET cc_start: 0.5863 (mpp) cc_final: 0.5352 (mpp) REVERT: I 35 GLN cc_start: 0.6685 (tp40) cc_final: 0.6262 (tp40) REVERT: I 59 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6980 (mtmm) REVERT: I 118 VAL cc_start: 0.7968 (t) cc_final: 0.7615 (p) REVERT: I 368 GLU cc_start: 0.8230 (pp20) cc_final: 0.7922 (pp20) REVERT: I 397 TYR cc_start: 0.5483 (m-80) cc_final: 0.5052 (m-80) REVERT: I 488 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: I 497 LYS cc_start: 0.8141 (tppt) cc_final: 0.7908 (tppt) REVERT: J 13 GLU cc_start: 0.8078 (mp0) cc_final: 0.7744 (mp0) REVERT: J 138 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7157 (mp-120) REVERT: J 181 PHE cc_start: 0.8480 (t80) cc_final: 0.8168 (t80) REVERT: J 211 LYS cc_start: 0.5221 (mttt) cc_final: 0.3707 (mmmt) REVERT: J 219 TRP cc_start: 0.6426 (m-90) cc_final: 0.5683 (m-90) REVERT: J 256 ILE cc_start: 0.6164 (mp) cc_final: 0.4296 (mt) REVERT: J 271 LYS cc_start: 0.9149 (tptt) cc_final: 0.8761 (tptt) REVERT: M 1 MET cc_start: 0.5558 (ppp) cc_final: 0.5352 (ppp) REVERT: M 52 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7692 (mm) REVERT: M 97 THR cc_start: 0.8615 (p) cc_final: 0.8348 (t) REVERT: M 106 PHE cc_start: 0.1027 (OUTLIER) cc_final: 0.0421 (m-80) REVERT: M 150 TYR cc_start: 0.5793 (t80) cc_final: 0.5500 (t80) REVERT: M 249 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7956 (mm-30) REVERT: M 358 PHE cc_start: 0.7276 (m-10) cc_final: 0.6851 (m-10) REVERT: M 384 VAL cc_start: 0.8558 (t) cc_final: 0.7733 (m) REVERT: M 386 VAL cc_start: 0.8232 (t) cc_final: 0.7809 (m) REVERT: M 435 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6765 (tmm) REVERT: M 436 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6421 (mt-10) REVERT: N 181 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.5872 (p90) REVERT: N 192 TRP cc_start: 0.7366 (p-90) cc_final: 0.7120 (p-90) REVERT: N 287 MET cc_start: 0.6472 (tpt) cc_final: 0.6159 (tpt) REVERT: N 321 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7725 (t80) REVERT: N 374 ARG cc_start: 0.7663 (ptm-80) cc_final: 0.7427 (ptm-80) REVERT: N 409 LYS cc_start: 0.6637 (mttt) cc_final: 0.6349 (mmtp) REVERT: N 414 MET cc_start: 0.6851 (mmm) cc_final: 0.6295 (mmm) outliers start: 141 outliers final: 110 residues processed: 686 average time/residue: 0.2162 time to fit residues: 238.7702 Evaluate side-chains 710 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 585 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 129 ASN 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 244 ASP 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 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 485 LYS 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 234 ASN Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 262 GLN 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 43 VAL Chi-restraints excluded: chain E residue 52 ILE 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 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 135 PHE Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 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 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 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 219 ILE 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 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 118 ILE Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR 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 43 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE 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 426 VAL Chi-restraints excluded: chain M residue 435 MET 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 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 115 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 293 TYR Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE 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: 0.1980 chunk 267 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 0.0770 chunk 55 optimal weight: 0.4980 chunk 213 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 370 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** I 430 GLN ** 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 35 GLN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 405 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 = 0.4643 r_free = 0.4643 target = 0.183284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.150961 restraints weight = 70572.037| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 4.35 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35032 Z= 0.158 Angle : 0.841 20.835 48160 Z= 0.404 Chirality : 0.063 1.028 5276 Planarity : 0.005 0.121 5488 Dihedral : 19.326 178.469 6068 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: -1.67 (0.13), residues: 3636 helix: -0.06 (0.14), residues: 1280 sheet: -1.46 (0.22), residues: 504 loop : -1.76 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 113 TYR 0.033 0.001 TYR E 6 PHE 0.033 0.001 PHE A 30 TRP 0.047 0.002 TRP J 369 HIS 0.028 0.001 HIS I 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (35032) covalent geometry : angle 0.84054 / 0.40 (48160) hydrogen bonds : bond 0.04189 / 2.70 ( 1128) hydrogen bonds : angle 5.28806 / 3.68 ( 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 732 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 596 time to evaluate : 1.202 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: A 19 LYS cc_start: 0.8079 (mttt) cc_final: 0.7673 (mttp) REVERT: A 64 ILE cc_start: 0.6331 (tp) cc_final: 0.6106 (tp) REVERT: A 225 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7303 (ttp-110) REVERT: A 234 PHE cc_start: 0.6730 (m-10) cc_final: 0.6520 (m-10) REVERT: A 262 TYR cc_start: 0.8313 (t80) cc_final: 0.7775 (t80) REVERT: A 356 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 406 MET cc_start: 0.7135 (tmm) cc_final: 0.6859 (tmm) REVERT: A 435 MET cc_start: 0.7760 (tpp) cc_final: 0.7528 (tpp) REVERT: A 458 ASP cc_start: 0.7482 (m-30) cc_final: 0.7231 (m-30) REVERT: A 485 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.5932 (mmtt) REVERT: B 14 ASP cc_start: 0.8690 (t0) cc_final: 0.8270 (t0) REVERT: B 105 TYR cc_start: 0.7242 (t80) cc_final: 0.6896 (t80) REVERT: B 119 ASP cc_start: 0.8719 (t0) cc_final: 0.8466 (t0) REVERT: B 193 ARG cc_start: 0.6103 (ptt-90) cc_final: 0.5884 (ptp90) REVERT: B 219 TRP cc_start: 0.6610 (m100) cc_final: 0.5474 (m100) REVERT: B 262 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8424 (mp10) REVERT: B 283 ARG cc_start: 0.7876 (mmm160) cc_final: 0.7347 (mmm160) REVERT: B 343 PHE cc_start: 0.8300 (m-80) cc_final: 0.8001 (m-10) REVERT: B 352 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8671 (mmtm) REVERT: E 135 ARG cc_start: 0.6314 (tpt90) cc_final: 0.5893 (tpt-90) REVERT: E 205 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6894 (tm-30) REVERT: E 227 SER cc_start: 0.6439 (p) cc_final: 0.6095 (p) REVERT: E 249 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7434 (tp30) REVERT: E 286 LYS cc_start: 0.7748 (tptp) cc_final: 0.7447 (tppt) REVERT: E 364 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.5798 (mtm-85) REVERT: E 503 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.4419 (t80) REVERT: F 13 GLU cc_start: 0.7525 (mp0) cc_final: 0.7192 (mp0) REVERT: F 72 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5650 (tm-30) REVERT: F 89 GLN cc_start: 0.8229 (pm20) cc_final: 0.7909 (pm20) REVERT: F 111 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7615 (tp30) REVERT: F 135 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.5178 (t80) REVERT: F 157 ILE cc_start: 0.4945 (OUTLIER) cc_final: 0.4600 (tt) REVERT: F 169 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6341 (mm-30) REVERT: F 240 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.7110 (mpp80) REVERT: F 277 MET cc_start: 0.8020 (tmm) cc_final: 0.7493 (tmm) REVERT: F 289 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8595 (mmtt) REVERT: F 304 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8469 (tppt) REVERT: F 324 SER cc_start: 0.8246 (t) cc_final: 0.7736 (p) REVERT: F 329 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7597 (mt) REVERT: F 336 MET cc_start: 0.5791 (mpp) cc_final: 0.5304 (mpp) REVERT: I 35 GLN cc_start: 0.6608 (tp40) cc_final: 0.6188 (tp40) REVERT: I 59 LYS cc_start: 0.7194 (mtpp) cc_final: 0.6980 (mtmm) REVERT: I 85 LYS cc_start: 0.7512 (pttt) cc_final: 0.7239 (ptmm) REVERT: I 118 VAL cc_start: 0.7909 (t) cc_final: 0.7569 (p) REVERT: I 368 GLU cc_start: 0.8154 (pp20) cc_final: 0.7885 (pp20) REVERT: I 397 TYR cc_start: 0.5343 (m-80) cc_final: 0.5001 (m-80) REVERT: I 488 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: I 497 LYS cc_start: 0.8124 (tppt) cc_final: 0.7895 (tppt) REVERT: J 13 GLU cc_start: 0.8060 (mp0) cc_final: 0.7759 (mp0) REVERT: J 138 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7097 (mp-120) REVERT: J 181 PHE cc_start: 0.8485 (t80) cc_final: 0.8152 (t80) REVERT: J 211 LYS cc_start: 0.5639 (mttt) cc_final: 0.4414 (mmtt) REVERT: J 219 TRP cc_start: 0.6417 (m-90) cc_final: 0.5674 (m-90) REVERT: J 256 ILE cc_start: 0.6163 (mp) cc_final: 0.4315 (mt) REVERT: J 271 LYS cc_start: 0.9144 (tptt) cc_final: 0.8794 (tptt) REVERT: J 277 MET cc_start: 0.7816 (mmm) cc_final: 0.7479 (mmm) REVERT: M 1 MET cc_start: 0.5572 (ppp) cc_final: 0.5370 (ppp) REVERT: M 52 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7695 (mm) REVERT: M 82 PHE cc_start: 0.8149 (m-10) cc_final: 0.7599 (m-10) REVERT: M 97 THR cc_start: 0.8619 (p) cc_final: 0.8346 (t) REVERT: M 106 PHE cc_start: 0.0806 (OUTLIER) cc_final: 0.0161 (m-80) REVERT: M 150 TYR cc_start: 0.5807 (t80) cc_final: 0.5560 (t80) REVERT: M 249 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8024 (mm-30) REVERT: M 355 LYS cc_start: 0.6950 (mtmt) cc_final: 0.6502 (tptm) REVERT: M 358 PHE cc_start: 0.7264 (m-10) cc_final: 0.6840 (m-10) REVERT: M 384 VAL cc_start: 0.8549 (t) cc_final: 0.7728 (m) REVERT: M 386 VAL cc_start: 0.8214 (t) cc_final: 0.7792 (m) REVERT: M 435 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6703 (tmm) REVERT: M 436 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6405 (mt-10) REVERT: N 181 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5882 (p90) REVERT: N 287 MET cc_start: 0.6520 (tpt) cc_final: 0.6205 (tpt) REVERT: N 321 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7722 (t80) REVERT: N 374 ARG cc_start: 0.7650 (ptm-80) cc_final: 0.7422 (ptm-80) REVERT: N 405 ASN cc_start: 0.6208 (OUTLIER) cc_final: 0.5674 (t0) REVERT: N 409 LYS cc_start: 0.6620 (mttt) cc_final: 0.6329 (mmtp) REVERT: N 414 MET cc_start: 0.6773 (mmm) cc_final: 0.6225 (mmm) outliers start: 136 outliers final: 104 residues processed: 675 average time/residue: 0.2130 time to fit residues: 231.9105 Evaluate side-chains 708 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 587 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 ASN 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 244 ASP 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 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 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 62 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 262 GLN 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 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 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 135 PHE Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 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 329 LEU 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 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 437 VAL 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 138 GLN Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR 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 401 ILE Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 426 VAL Chi-restraints excluded: chain M residue 435 MET 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 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 115 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 293 TYR Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 387 ASP Chi-restraints excluded: chain N residue 405 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 210 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 364 optimal weight: 20.0000 chunk 227 optimal weight: 0.0060 chunk 154 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.183300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.151013 restraints weight = 70230.838| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 4.35 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 35032 Z= 0.182 Angle : 0.916 59.200 48160 Z= 0.465 Chirality : 0.063 1.028 5276 Planarity : 0.005 0.118 5488 Dihedral : 19.324 178.490 6068 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.05 % Allowed : 33.26 % Favored : 62.68 % Cbeta Deviations : 0.03 % 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: -1.66 (0.13), residues: 3636 helix: -0.05 (0.14), residues: 1280 sheet: -1.46 (0.22), residues: 504 loop : -1.76 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 113 TYR 0.029 0.001 TYR E 6 PHE 0.031 0.001 PHE A 30 TRP 0.040 0.002 TRP J 369 HIS 0.067 0.002 HIS I 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (35032) covalent geometry : angle 0.91644 / 0.47 (48160) hydrogen bonds : bond 0.04196 / 2.70 ( 1128) hydrogen bonds : angle 5.28979 / 3.68 ( 3145) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7813.27 seconds wall clock time: 135 minutes 33.61 seconds (8133.61 seconds total)