Starting phenix.real_space_refine on Sat Jun 28 22:38:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8it1_35703/06_2025/8it1_35703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8it1_35703/06_2025/8it1_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_35703/06_2025/8it1_35703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8it1_35703/06_2025/8it1_35703.map" model { file = "/net/cci-nas-00/data/ceres_data/8it1_35703/06_2025/8it1_35703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8it1_35703/06_2025/8it1_35703.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33844 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "J" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "N" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "O" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "P" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "C" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "G" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "H" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Time building chain proxies: 20.68, per 1000 atoms: 0.61 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: 8.47 Conformation dependent library (CDL) restraints added in 3.9 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: 10.98 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: 13.45 Time building geometry restraints manager: 10.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7993 1.33 - 1.45: 8059 1.45 - 1.57: 18488 1.57 - 1.69: 352 1.69 - 1.81: 140 Bond restraints: 35032 Sorted by residual: bond pdb=" CB ASN N 435 " pdb=" CG ASN N 435 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.99e+00 bond pdb=" CB MET M 406 " pdb=" CG MET M 406 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB ASN M 90 " pdb=" CG ASN M 90 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.58e+00 bond pdb=" CB ASN B 435 " pdb=" CG ASN B 435 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.20e+00 bond pdb=" CE LYS I 325 " pdb=" NZ LYS I 325 " ideal model delta sigma weight residual 1.489 1.445 0.044 3.00e-02 1.11e+03 2.15e+00 ... (remaining 35027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 47980 3.92 - 7.84: 150 7.84 - 11.77: 26 11.77 - 15.69: 3 15.69 - 19.61: 1 Bond angle restraints: 48160 Sorted by residual: angle pdb=" CA LEU I 210 " pdb=" CB LEU I 210 " pdb=" CG LEU I 210 " ideal model delta sigma weight residual 116.30 135.91 -19.61 3.50e+00 8.16e-02 3.14e+01 angle pdb=" CA MET F 277 " pdb=" CB MET F 277 " pdb=" CG MET F 277 " ideal model delta sigma weight residual 114.10 124.38 -10.28 2.00e+00 2.50e-01 2.64e+01 angle pdb=" CA MET F 92 " pdb=" CB MET F 92 " pdb=" CG MET F 92 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA LEU N 268 " pdb=" CB LEU N 268 " pdb=" CG LEU N 268 " ideal model delta sigma weight residual 116.30 131.48 -15.18 3.50e+00 8.16e-02 1.88e+01 angle pdb=" CA GLU I 488 " pdb=" CB GLU I 488 " pdb=" CG GLU I 488 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 ... (remaining 48155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 16802 18.17 - 36.33: 2827 36.33 - 54.50: 1017 54.50 - 72.67: 280 72.67 - 90.84: 50 Dihedral angle restraints: 20976 sinusoidal: 10196 harmonic: 10780 Sorted by residual: dihedral pdb=" CA MET M 406 " pdb=" C MET M 406 " pdb=" N ARG M 407 " pdb=" CA ARG M 407 " ideal model delta harmonic sigma weight residual 180.00 148.05 31.95 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA VAL E 317 " pdb=" C VAL E 317 " pdb=" N GLY E 318 " pdb=" CA GLY E 318 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA VAL I 317 " pdb=" C VAL I 317 " pdb=" N GLY I 318 " pdb=" CA GLY I 318 " ideal model delta harmonic sigma weight residual 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 20973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4785 0.080 - 0.160: 476 0.160 - 0.240: 14 0.240 - 0.320: 0 0.320 - 0.400: 1 Chirality restraints: 5276 Sorted by residual: chirality pdb=" CB ILE F 433 " pdb=" CA ILE F 433 " pdb=" CG1 ILE F 433 " pdb=" CG2 ILE F 433 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA TYR F 330 " pdb=" N TYR F 330 " pdb=" C TYR F 330 " pdb=" CB TYR F 330 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 49 " pdb=" CA ILE B 49 " pdb=" CG1 ILE B 49 " pdb=" CG2 ILE B 49 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 5273 not shown) Planarity restraints: 5488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO E 332 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 143 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO I 144 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 144 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 144 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 362 " 0.237 9.50e-02 1.11e+02 1.06e-01 7.27e+00 pdb=" NE ARG I 362 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG I 362 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 362 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 362 " 0.012 2.00e-02 2.50e+03 ... (remaining 5485 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4275 2.75 - 3.29: 33488 3.29 - 3.82: 61314 3.82 - 4.36: 68151 4.36 - 4.90: 111853 Nonbonded interactions: 279081 Sorted by model distance: nonbonded pdb=" OG SER N 359 " pdb=" OP1 DA O 44 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN I 90 " pdb=" OH TYR M 37 " model vdw 2.227 3.040 nonbonded pdb=" O4 DT C 26 " pdb=" O6 G D 20 " model vdw 2.230 2.432 nonbonded pdb=" O4 DT K 26 " pdb=" O6 G L 20 " model vdw 2.231 2.432 nonbonded pdb=" OH TYR J 221 " pdb=" O GLU J 231 " model vdw 2.235 3.040 ... (remaining 279076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 82.560 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35032 Z= 0.221 Angle : 0.727 19.610 48160 Z= 0.381 Chirality : 0.046 0.400 5276 Planarity : 0.006 0.106 5488 Dihedral : 20.585 90.836 14008 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (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 TRP 0.017 0.001 TRP I 86 HIS 0.012 0.001 HIS I 207 PHE 0.024 0.001 PHE B 273 TYR 0.013 0.001 TYR M 285 ARG 0.010 0.001 ARG I 362 Details of bonding type rmsd hydrogen bonds : bond 0.19052 ( 1128) hydrogen bonds : angle 7.74851 ( 3145) covalent geometry : bond 0.00484 (35032) covalent geometry : angle 0.72674 (48160) *********************** 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 : 3.713 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: 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: 0.7044 (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: 0.3766 (tm-30) REVERT: I 422 THR cc_start: 0.7126 (p) cc_final: 0.6918 (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: 0.5215 (m-10) 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: 0.5645 time to fit residues: 679.7189 Evaluate side-chains 591 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 590 time to evaluate : 3.688 ------------------------------------------------------------------------------- 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 320 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 181 optimal weight: 0.0980 chunk 221 optimal weight: 1.9990 chunk 345 optimal weight: 0.7980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 251 HIS ** A 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 122 ASN E 209 GLN E 374 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 349 GLN J 69 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN M 35 GLN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN N 69 ASN ** N 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 258 ASN N 270 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.182814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.150134 restraints weight = 69681.510| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 4.23 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35032 Z= 0.258 Angle : 0.765 11.363 48160 Z= 0.409 Chirality : 0.048 0.305 5276 Planarity : 0.006 0.070 5488 Dihedral : 18.727 81.523 6389 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.34 % Allowed : 28.93 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3636 helix: -0.37 (0.14), residues: 1312 sheet: -1.62 (0.21), residues: 586 loop : -1.74 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP I 86 HIS 0.011 0.002 HIS I 111 PHE 0.029 0.002 PHE F 45 TYR 0.022 0.002 TYR F 293 ARG 0.007 0.001 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 1128) hydrogen bonds : angle 5.84167 ( 3145) covalent geometry : bond 0.00587 (35032) covalent geometry : angle 0.76505 (48160) *********************** 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 854 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 679 time to evaluate : 3.992 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 64 ILE cc_start: 0.6740 (tp) cc_final: 0.6351 (tp) REVERT: A 87 GLU cc_start: 0.7064 (mp0) cc_final: 0.6335 (mp0) REVERT: A 117 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7154 (mt) REVERT: A 136 VAL cc_start: 0.8384 (t) cc_final: 0.8175 (t) REVERT: A 225 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7428 (ttp-110) REVERT: A 251 HIS cc_start: 0.6098 (OUTLIER) cc_final: 0.5743 (m90) REVERT: A 262 TYR cc_start: 0.8426 (t80) cc_final: 0.8131 (t80) REVERT: A 270 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6921 (ptmt) REVERT: A 279 CYS cc_start: 0.7840 (t) cc_final: 0.7160 (m) REVERT: A 305 LEU cc_start: 0.7721 (pp) cc_final: 0.7372 (tt) REVERT: A 383 LEU cc_start: 0.8364 (pt) cc_final: 0.8084 (pt) REVERT: B 13 GLU cc_start: 0.8531 (mp0) cc_final: 0.8328 (mp0) REVERT: B 14 ASP cc_start: 0.8576 (t0) cc_final: 0.8243 (t0) REVERT: B 159 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 205 PHE cc_start: 0.7508 (m-10) cc_final: 0.7266 (m-10) REVERT: B 275 LEU cc_start: 0.8410 (mt) cc_final: 0.7967 (mp) REVERT: E 74 MET cc_start: 0.6421 (pmm) cc_final: 0.6218 (pmm) REVERT: E 117 LEU cc_start: 0.7018 (tp) cc_final: 0.6669 (tt) REVERT: E 149 LYS cc_start: 0.6737 (tptt) cc_final: 0.6339 (tppt) REVERT: E 205 GLN cc_start: 0.6888 (tm-30) cc_final: 0.6174 (tm-30) REVERT: E 331 LYS cc_start: 0.8363 (tptt) cc_final: 0.7819 (tptt) REVERT: F 13 GLU cc_start: 0.7272 (mp0) cc_final: 0.6782 (mp0) REVERT: F 89 GLN cc_start: 0.8228 (pm20) cc_final: 0.7824 (pm20) REVERT: F 135 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.5379 (t80) REVERT: F 161 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5716 (m-30) REVERT: F 174 ASN cc_start: 0.8228 (t0) cc_final: 0.7857 (t0) REVERT: F 250 ARG cc_start: 0.8170 (tpm170) cc_final: 0.7760 (tpm170) REVERT: F 294 TRP cc_start: 0.6518 (p-90) cc_final: 0.5893 (p-90) REVERT: I 1 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6665 (tpt) REVERT: I 8 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: I 35 GLN cc_start: 0.6529 (tp40) cc_final: 0.6121 (tp40) REVERT: I 303 MET cc_start: 0.8009 (tmm) cc_final: 0.7430 (tmm) REVERT: I 443 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7140 (mt) REVERT: I 446 ASN cc_start: 0.5843 (OUTLIER) cc_final: 0.5301 (m110) REVERT: J 13 GLU cc_start: 0.8073 (mp0) cc_final: 0.7682 (mp0) REVERT: J 181 PHE cc_start: 0.8382 (t80) cc_final: 0.8143 (t80) REVERT: J 271 LYS cc_start: 0.9163 (tptt) cc_final: 0.8832 (tptt) REVERT: J 274 GLU cc_start: 0.8504 (pp20) cc_final: 0.8189 (pp20) REVERT: J 433 ILE cc_start: 0.7387 (pt) cc_final: 0.7019 (mt) REVERT: J 445 GLU cc_start: 0.4091 (OUTLIER) cc_final: 0.3707 (pp20) REVERT: M 72 ARG cc_start: 0.5380 (OUTLIER) cc_final: 0.4819 (mtm-85) REVERT: M 79 GLU cc_start: 0.8046 (pm20) cc_final: 0.7775 (mp0) REVERT: M 95 GLU cc_start: 0.7857 (tp30) cc_final: 0.7303 (tm-30) REVERT: M 358 PHE cc_start: 0.7318 (m-10) cc_final: 0.6873 (m-10) REVERT: M 384 VAL cc_start: 0.8431 (t) cc_final: 0.7751 (m) REVERT: M 386 VAL cc_start: 0.8133 (t) cc_final: 0.7702 (m) REVERT: M 435 MET cc_start: 0.7675 (tmm) cc_final: 0.7172 (tmm) REVERT: M 436 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6923 (mt-10) REVERT: M 474 ASP cc_start: 0.6344 (t0) cc_final: 0.4809 (t0) REVERT: M 481 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7438 (tpp80) REVERT: N 205 PHE cc_start: 0.7173 (t80) cc_final: 0.6882 (t80) REVERT: N 233 TYR cc_start: 0.7212 (t80) cc_final: 0.6934 (t80) REVERT: N 318 TYR cc_start: 0.3495 (OUTLIER) cc_final: 0.3150 (m-80) REVERT: N 340 HIS cc_start: 0.8422 (m-70) cc_final: 0.8180 (m-70) REVERT: N 376 LYS cc_start: 0.7549 (mptt) cc_final: 0.7177 (mmtm) REVERT: N 409 LYS cc_start: 0.6804 (mttt) cc_final: 0.6505 (mmtp) outliers start: 175 outliers final: 83 residues processed: 798 average time/residue: 0.5066 time to fit residues: 638.7901 Evaluate side-chains 696 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 600 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 LYS 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 443 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 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 159 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 ASN 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 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 141 VAL 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 406 MET 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 58 CYS Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 229 LYS 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 395 VAL 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 1 MET 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 126 ILE Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 332 SER Chi-restraints excluded: chain J residue 336 MET Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 409 ASN 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 M residue 504 LYS 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 103 LEU Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 258 ASN 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 279 optimal weight: 0.0970 chunk 285 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 318 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 251 HIS B 320 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN N 262 GLN N 270 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.186093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.153850 restraints weight = 70021.962| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 4.29 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35032 Z= 0.143 Angle : 0.646 12.879 48160 Z= 0.342 Chirality : 0.044 0.317 5276 Planarity : 0.005 0.062 5488 Dihedral : 18.730 86.016 6389 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.21 % Allowed : 29.60 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3636 helix: -0.12 (0.14), residues: 1276 sheet: -1.61 (0.21), residues: 552 loop : -1.71 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 369 HIS 0.020 0.001 HIS A 251 PHE 0.025 0.001 PHE A 30 TYR 0.032 0.001 TYR I 397 ARG 0.006 0.001 ARG N 361 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1128) hydrogen bonds : angle 5.50882 ( 3145) covalent geometry : bond 0.00329 (35032) covalent geometry : angle 0.64607 (48160) *********************** 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 811 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 640 time to evaluate : 5.395 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: A 64 ILE cc_start: 0.6642 (tp) cc_final: 0.6328 (tp) REVERT: A 87 GLU cc_start: 0.6938 (mp0) cc_final: 0.6549 (mp0) REVERT: A 100 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5885 (tm-30) REVERT: A 117 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7218 (mt) REVERT: A 136 VAL cc_start: 0.8281 (t) cc_final: 0.8073 (t) REVERT: A 225 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7348 (ttp-110) REVERT: A 262 TYR cc_start: 0.8311 (t80) cc_final: 0.7856 (t80) REVERT: A 270 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6855 (ptpt) REVERT: A 442 PHE cc_start: 0.7590 (t80) cc_final: 0.7311 (t80) REVERT: A 458 ASP cc_start: 0.7361 (m-30) cc_final: 0.7023 (m-30) REVERT: B 14 ASP cc_start: 0.8486 (t0) cc_final: 0.8099 (t0) REVERT: B 16 ASP cc_start: 0.8243 (p0) cc_final: 0.7926 (p0) REVERT: B 171 TYR cc_start: 0.7223 (m-80) cc_final: 0.7007 (m-80) REVERT: B 283 ARG cc_start: 0.7605 (mmm160) cc_final: 0.7316 (mmm160) REVERT: B 352 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8471 (mmtm) REVERT: B 366 LYS cc_start: 0.6984 (mtmt) cc_final: 0.6768 (mttt) REVERT: E 50 LEU cc_start: 0.7379 (mt) cc_final: 0.7135 (mt) REVERT: E 74 MET cc_start: 0.6390 (pmm) cc_final: 0.6086 (pmm) REVERT: E 135 ARG cc_start: 0.6962 (tpt90) cc_final: 0.6499 (ttt-90) REVERT: E 322 ASN cc_start: 0.7163 (t0) cc_final: 0.6680 (t0) REVERT: E 331 LYS cc_start: 0.8164 (tptt) cc_final: 0.7741 (tptt) REVERT: E 364 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.5781 (mtm-85) REVERT: E 430 GLN cc_start: 0.3433 (mm-40) cc_final: 0.3125 (tm-30) REVERT: F 1 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7932 (ptp) REVERT: F 13 GLU cc_start: 0.7293 (mp0) cc_final: 0.6662 (mp0) REVERT: F 52 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6548 (mt-10) REVERT: F 89 GLN cc_start: 0.8137 (pm20) cc_final: 0.7799 (pm20) REVERT: F 111 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7419 (tp30) REVERT: F 119 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7978 (p0) REVERT: F 135 PHE cc_start: 0.5690 (OUTLIER) cc_final: 0.5090 (t80) REVERT: F 147 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8789 (p-80) REVERT: F 174 ASN cc_start: 0.8226 (t0) cc_final: 0.7979 (t0) REVERT: F 240 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6738 (mpp80) REVERT: F 294 TRP cc_start: 0.6423 (p-90) cc_final: 0.5739 (p-90) REVERT: F 304 LYS cc_start: 0.8964 (tppt) cc_final: 0.8596 (mmmm) REVERT: F 336 MET cc_start: 0.5762 (mpp) cc_final: 0.5000 (mpp) REVERT: F 402 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8006 (pp) REVERT: I 8 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: I 35 GLN cc_start: 0.6413 (tp40) cc_final: 0.5961 (tp40) REVERT: I 85 LYS cc_start: 0.7185 (pptt) cc_final: 0.6839 (pptt) REVERT: I 446 ASN cc_start: 0.5569 (OUTLIER) cc_final: 0.4758 (m110) REVERT: I 488 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: J 13 GLU cc_start: 0.7962 (mp0) cc_final: 0.7612 (mp0) REVERT: J 86 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8755 (mtpt) REVERT: J 171 TYR cc_start: 0.7502 (m-80) cc_final: 0.7005 (m-80) REVERT: J 181 PHE cc_start: 0.8473 (t80) cc_final: 0.8131 (t80) REVERT: J 211 LYS cc_start: 0.5983 (mttt) cc_final: 0.4576 (mmmt) REVERT: J 229 LYS cc_start: 0.8189 (pttt) cc_final: 0.7784 (pttt) REVERT: J 271 LYS cc_start: 0.9176 (tptt) cc_final: 0.8808 (tptt) REVERT: J 277 MET cc_start: 0.7838 (mmm) cc_final: 0.7627 (mmm) REVERT: J 445 GLU cc_start: 0.3857 (OUTLIER) cc_final: 0.3560 (mm-30) REVERT: M 52 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7670 (mm) REVERT: M 72 ARG cc_start: 0.5328 (OUTLIER) cc_final: 0.5007 (mtm-85) REVERT: M 79 GLU cc_start: 0.7895 (pm20) cc_final: 0.7652 (mp0) REVERT: M 95 GLU cc_start: 0.7922 (tp30) cc_final: 0.7367 (tm-30) REVERT: M 146 GLU cc_start: 0.7091 (mp0) cc_final: 0.6874 (mp0) REVERT: M 358 PHE cc_start: 0.7293 (m-10) cc_final: 0.6844 (m-10) REVERT: M 384 VAL cc_start: 0.8411 (t) cc_final: 0.7701 (m) REVERT: M 386 VAL cc_start: 0.8134 (t) cc_final: 0.7680 (m) REVERT: M 435 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6758 (tmm) REVERT: M 436 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7021 (mt-10) REVERT: N 13 GLU cc_start: 0.7396 (mp0) cc_final: 0.7195 (mp0) REVERT: N 118 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (tt) REVERT: N 205 PHE cc_start: 0.7191 (t80) cc_final: 0.6896 (t80) REVERT: N 321 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7609 (t80) REVERT: N 409 LYS cc_start: 0.6685 (mttt) cc_final: 0.6408 (mmtp) outliers start: 171 outliers final: 94 residues processed: 741 average time/residue: 0.5971 time to fit residues: 699.9093 Evaluate side-chains 709 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 597 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 LEU 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 288 ILE 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 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 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 227 LEU Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 LYS Chi-restraints excluded: chain F residue 378 LEU 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 126 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 271 LEU 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 445 ILE Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 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 52 ILE Chi-restraints excluded: chain M residue 72 ARG 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 387 THR Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 435 MET 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 32 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 349 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 355 optimal weight: 5.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS A 430 GLN A 454 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 349 GLN M 35 GLN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 HIS N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.184788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.152329 restraints weight = 69330.086| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 4.29 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35032 Z= 0.150 Angle : 0.639 13.413 48160 Z= 0.337 Chirality : 0.044 0.280 5276 Planarity : 0.005 0.061 5488 Dihedral : 18.699 85.848 6389 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.43 % Allowed : 30.21 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3636 helix: -0.09 (0.14), residues: 1280 sheet: -1.46 (0.21), residues: 576 loop : -1.67 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 320 HIS 0.015 0.001 HIS A 251 PHE 0.028 0.002 PHE N 411 TYR 0.020 0.001 TYR E 6 ARG 0.009 0.001 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1128) hydrogen bonds : angle 5.37674 ( 3145) covalent geometry : bond 0.00348 (35032) covalent geometry : angle 0.63891 (48160) *********************** 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 799 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 621 time to evaluate : 3.349 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 1 MET cc_start: 0.2285 (tpp) cc_final: 0.1413 (tpt) REVERT: A 64 ILE cc_start: 0.6512 (tp) cc_final: 0.6253 (tp) REVERT: A 87 GLU cc_start: 0.7029 (mp0) cc_final: 0.6592 (mp0) REVERT: A 146 GLU cc_start: 0.7451 (pm20) cc_final: 0.7102 (tp30) REVERT: A 225 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7281 (ttp-110) REVERT: A 262 TYR cc_start: 0.8385 (t80) cc_final: 0.7925 (t80) REVERT: A 270 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6920 (ptpt) REVERT: A 447 LYS cc_start: 0.7867 (mptt) cc_final: 0.6743 (mptt) REVERT: A 458 ASP cc_start: 0.7458 (m-30) cc_final: 0.7111 (m-30) REVERT: B 13 GLU cc_start: 0.8495 (mp0) cc_final: 0.8287 (mp0) REVERT: B 14 ASP cc_start: 0.8581 (t0) cc_final: 0.8175 (t0) REVERT: B 171 TYR cc_start: 0.7223 (m-80) cc_final: 0.6940 (m-80) REVERT: B 219 TRP cc_start: 0.6471 (m100) cc_final: 0.5110 (m100) REVERT: B 283 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7373 (mmm160) REVERT: B 308 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5840 (tt) REVERT: B 352 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8560 (mmtm) REVERT: B 376 LYS cc_start: 0.7847 (mttm) cc_final: 0.7618 (mmmm) REVERT: B 408 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6537 (tt) REVERT: E 50 LEU cc_start: 0.7389 (mt) cc_final: 0.7076 (mt) REVERT: E 135 ARG cc_start: 0.7084 (tpt90) cc_final: 0.6570 (ttt-90) REVERT: E 205 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6154 (tm-30) REVERT: E 296 ASN cc_start: 0.5496 (m-40) cc_final: 0.5196 (m-40) REVERT: E 364 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.5845 (mtm-85) REVERT: E 369 GLU cc_start: 0.8055 (pt0) cc_final: 0.7358 (pt0) REVERT: E 503 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.4004 (t80) REVERT: E 505 TYR cc_start: 0.6285 (m-80) cc_final: 0.6068 (m-80) REVERT: F 1 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7991 (ptp) REVERT: F 13 GLU cc_start: 0.7349 (mp0) cc_final: 0.6667 (mp0) REVERT: F 52 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6506 (mt-10) REVERT: F 72 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5588 (tm-30) REVERT: F 89 GLN cc_start: 0.8170 (pm20) cc_final: 0.7842 (pm20) REVERT: F 111 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7401 (tp30) REVERT: F 135 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.5061 (t80) REVERT: F 161 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.4866 (m-30) REVERT: F 294 TRP cc_start: 0.6348 (p-90) cc_final: 0.5658 (p-90) REVERT: F 304 LYS cc_start: 0.8862 (tppt) cc_final: 0.8594 (tppt) REVERT: F 336 MET cc_start: 0.5651 (mpp) cc_final: 0.5313 (mpp) REVERT: I 35 GLN cc_start: 0.6486 (tp40) cc_final: 0.6038 (tp40) REVERT: I 85 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6987 (pptt) REVERT: I 398 LYS cc_start: 0.7377 (tptt) cc_final: 0.6652 (tptt) REVERT: I 429 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7221 (tt) REVERT: I 446 ASN cc_start: 0.5587 (OUTLIER) cc_final: 0.4795 (m110) REVERT: I 476 GLU cc_start: 0.7577 (pm20) cc_final: 0.7261 (pm20) REVERT: I 488 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: J 13 GLU cc_start: 0.8009 (mp0) cc_final: 0.7599 (mp0) REVERT: J 130 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6326 (p0) REVERT: J 159 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7590 (tt) REVERT: J 167 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.6151 (pttt) REVERT: J 181 PHE cc_start: 0.8465 (t80) cc_final: 0.8113 (t80) REVERT: J 211 LYS cc_start: 0.6018 (mttt) cc_final: 0.4646 (mmmt) REVERT: J 256 ILE cc_start: 0.6175 (mp) cc_final: 0.4397 (mt) REVERT: J 271 LYS cc_start: 0.9193 (tptt) cc_final: 0.8799 (tptt) REVERT: J 362 ARG cc_start: 0.3417 (OUTLIER) cc_final: 0.2422 (mmp-170) REVERT: J 374 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7441 (ttt-90) REVERT: J 433 ILE cc_start: 0.7303 (pt) cc_final: 0.6975 (mt) REVERT: M 95 GLU cc_start: 0.7937 (tp30) cc_final: 0.7327 (tm-30) REVERT: M 146 GLU cc_start: 0.7264 (mp0) cc_final: 0.6950 (mp0) REVERT: M 262 TYR cc_start: 0.6463 (t80) cc_final: 0.6140 (t80) REVERT: M 384 VAL cc_start: 0.8426 (t) cc_final: 0.8089 (m) REVERT: M 386 VAL cc_start: 0.8148 (t) cc_final: 0.7739 (m) REVERT: M 436 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6784 (mt-10) REVERT: M 503 PHE cc_start: 0.5899 (t80) cc_final: 0.5579 (t80) REVERT: N 83 LYS cc_start: 0.8275 (tppp) cc_final: 0.8059 (mmmm) REVERT: N 181 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5748 (p90) REVERT: N 192 TRP cc_start: 0.7251 (p-90) cc_final: 0.6759 (p-90) REVERT: N 205 PHE cc_start: 0.7252 (t80) cc_final: 0.6923 (t80) REVERT: N 374 ARG cc_start: 0.7601 (ptm-80) cc_final: 0.7286 (ptm-80) REVERT: N 376 LYS cc_start: 0.7510 (mptt) cc_final: 0.7275 (mmtm) REVERT: N 409 LYS cc_start: 0.6658 (mttt) cc_final: 0.6381 (mmtp) REVERT: N 414 MET cc_start: 0.6906 (mmm) cc_final: 0.6280 (mmm) outliers start: 178 outliers final: 114 residues processed: 727 average time/residue: 0.5568 time to fit residues: 645.3905 Evaluate side-chains 717 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 585 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 122 ASN 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 251 HIS Chi-restraints excluded: chain A residue 270 LYS 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 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 216 THR 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 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 374 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 E residue 501 LEU Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 378 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 I residue 13 LEU Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 271 LEU 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 429 LEU 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 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 232 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 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 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 35 GLN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 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 M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain M residue 504 LYS Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 58 CYS Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 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 258 ASN Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 21 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 199 optimal weight: 0.1980 chunk 358 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 212 optimal weight: 0.0060 chunk 310 optimal weight: 1.9990 chunk 162 optimal weight: 0.0670 overall best weight: 0.8538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 349 GLN I 350 ASN ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN N 270 ASN ** 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 = 0.4612 r_free = 0.4612 target = 0.179576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.147541 restraints weight = 71858.645| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 4.20 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35032 Z= 0.166 Angle : 0.652 13.086 48160 Z= 0.344 Chirality : 0.044 0.271 5276 Planarity : 0.005 0.061 5488 Dihedral : 18.702 85.783 6389 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.76 % Allowed : 30.27 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3636 helix: -0.10 (0.14), residues: 1284 sheet: -1.50 (0.22), residues: 542 loop : -1.64 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 320 HIS 0.014 0.001 HIS A 251 PHE 0.033 0.002 PHE E 206 TYR 0.022 0.001 TYR E 6 ARG 0.009 0.001 ARG M 364 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1128) hydrogen bonds : angle 5.32500 ( 3145) covalent geometry : bond 0.00383 (35032) covalent geometry : angle 0.65206 (48160) *********************** 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 803 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 614 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2252 (tpp) cc_final: 0.1585 (tpt) REVERT: A 64 ILE cc_start: 0.6385 (tp) cc_final: 0.6116 (tp) REVERT: A 72 ARG cc_start: 0.6050 (mpp80) cc_final: 0.5712 (mpp-170) REVERT: A 87 GLU cc_start: 0.7033 (mp0) cc_final: 0.6508 (mp0) REVERT: A 100 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6335 (pt0) REVERT: A 146 GLU cc_start: 0.7525 (pm20) cc_final: 0.7278 (tp30) REVERT: A 205 GLN cc_start: 0.7441 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 262 TYR cc_start: 0.8406 (t80) cc_final: 0.7982 (t80) REVERT: A 270 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6950 (ptpt) REVERT: A 447 LYS cc_start: 0.7908 (mptt) cc_final: 0.7639 (mptt) REVERT: A 458 ASP cc_start: 0.7500 (m-30) cc_final: 0.7119 (m-30) REVERT: B 14 ASP cc_start: 0.8692 (t0) cc_final: 0.8302 (t0) REVERT: B 219 TRP cc_start: 0.6645 (m100) cc_final: 0.5414 (m100) REVERT: B 283 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7450 (mmm160) REVERT: B 352 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8702 (mmtm) REVERT: B 376 LYS cc_start: 0.7780 (mttm) cc_final: 0.7418 (mmtt) REVERT: E 135 ARG cc_start: 0.7117 (tpt90) cc_final: 0.6660 (ttt-90) REVERT: E 227 SER cc_start: 0.6604 (p) cc_final: 0.6270 (p) REVERT: E 263 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8095 (mmtt) REVERT: E 296 ASN cc_start: 0.5569 (m-40) cc_final: 0.5187 (m-40) REVERT: E 305 LEU cc_start: 0.7325 (pt) cc_final: 0.7088 (pt) REVERT: E 364 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.5896 (mtm-85) REVERT: E 369 GLU cc_start: 0.8052 (pt0) cc_final: 0.7505 (pt0) REVERT: E 476 GLU cc_start: 0.7173 (pm20) cc_final: 0.6691 (pm20) REVERT: E 503 PHE cc_start: 0.5828 (OUTLIER) cc_final: 0.4010 (t80) REVERT: E 505 TYR cc_start: 0.6273 (m-80) cc_final: 0.6031 (m-80) REVERT: F 1 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8079 (ptp) REVERT: F 13 GLU cc_start: 0.7423 (mp0) cc_final: 0.6702 (mp0) REVERT: F 52 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6513 (mt-10) REVERT: F 57 THR cc_start: 0.7792 (m) cc_final: 0.7591 (p) REVERT: F 72 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5703 (tm-30) REVERT: F 89 GLN cc_start: 0.8269 (pm20) cc_final: 0.7912 (pm20) REVERT: F 111 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7489 (tp30) REVERT: F 119 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8178 (p0) REVERT: F 135 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.5052 (t80) REVERT: F 157 ILE cc_start: 0.4958 (OUTLIER) cc_final: 0.4535 (tt) REVERT: F 169 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6386 (mm-30) REVERT: F 250 ARG cc_start: 0.8099 (tpm170) cc_final: 0.7543 (tpm170) REVERT: F 304 LYS cc_start: 0.8845 (tppt) cc_final: 0.8553 (tppt) REVERT: F 324 SER cc_start: 0.8294 (t) cc_final: 0.7760 (p) REVERT: F 336 MET cc_start: 0.5525 (mpp) cc_final: 0.5285 (mpp) REVERT: I 8 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: I 35 GLN cc_start: 0.6646 (tp40) cc_final: 0.6226 (tp40) REVERT: I 85 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7065 (pptt) REVERT: I 474 ASP cc_start: 0.4437 (t0) cc_final: 0.3877 (t0) REVERT: I 488 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6873 (pm20) REVERT: J 13 GLU cc_start: 0.8030 (mp0) cc_final: 0.7628 (mp0) REVERT: J 86 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8699 (mtpt) REVERT: J 130 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.6279 (p0) REVERT: J 159 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7661 (tt) REVERT: J 171 TYR cc_start: 0.7722 (m-80) cc_final: 0.7299 (m-80) REVERT: J 181 PHE cc_start: 0.8494 (t80) cc_final: 0.8157 (t80) REVERT: J 211 LYS cc_start: 0.5957 (mttt) cc_final: 0.4632 (mmmt) REVERT: J 256 ILE cc_start: 0.6158 (mp) cc_final: 0.4464 (mt) REVERT: J 271 LYS cc_start: 0.9239 (tptt) cc_final: 0.8872 (tptt) REVERT: J 362 ARG cc_start: 0.3533 (OUTLIER) cc_final: 0.2500 (mmp-170) REVERT: J 382 ARG cc_start: 0.7619 (mmt-90) cc_final: 0.7393 (mmt180) REVERT: M 52 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7713 (mm) REVERT: M 95 GLU cc_start: 0.7959 (tp30) cc_final: 0.7450 (tm-30) REVERT: M 106 PHE cc_start: 0.0777 (OUTLIER) cc_final: 0.0090 (m-80) REVERT: M 355 LYS cc_start: 0.7179 (mtmt) cc_final: 0.6687 (tptm) REVERT: M 358 PHE cc_start: 0.7389 (m-10) cc_final: 0.6895 (m-10) REVERT: M 382 ASN cc_start: 0.7740 (m-40) cc_final: 0.7519 (m-40) REVERT: M 384 VAL cc_start: 0.8546 (t) cc_final: 0.7822 (m) REVERT: M 386 VAL cc_start: 0.8261 (t) cc_final: 0.7824 (m) REVERT: M 503 PHE cc_start: 0.5901 (t80) cc_final: 0.5489 (t80) REVERT: N 83 LYS cc_start: 0.8239 (tppp) cc_final: 0.7963 (mmmm) REVERT: N 181 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5612 (p90) REVERT: N 192 TRP cc_start: 0.7320 (p-90) cc_final: 0.6894 (p-90) REVERT: N 233 TYR cc_start: 0.6986 (t80) cc_final: 0.6784 (t80) REVERT: N 321 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7696 (t80) REVERT: N 337 VAL cc_start: 0.5680 (OUTLIER) cc_final: 0.5325 (t) REVERT: N 409 LYS cc_start: 0.6685 (mttt) cc_final: 0.6399 (mmtp) outliers start: 189 outliers final: 123 residues processed: 733 average time/residue: 0.4991 time to fit residues: 580.1806 Evaluate side-chains 728 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 585 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 216 THR 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 282 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 423 LEU 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 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 153 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 375 GLU 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 85 LYS 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 271 LEU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 350 ASN Chi-restraints excluded: chain I residue 383 LEU 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 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 188 HIS Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU 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 291 PHE 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 55 SER Chi-restraints excluded: chain M residue 106 PHE 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 M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain M residue 504 LYS Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 58 CYS 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 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 258 ASN Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 337 VAL 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 209 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 214 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS I 302 GLN I 349 GLN ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 360 HIS N 258 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.181726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.149888 restraints weight = 69084.791| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 4.15 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35032 Z= 0.156 Angle : 0.662 14.671 48160 Z= 0.347 Chirality : 0.044 0.254 5276 Planarity : 0.005 0.061 5488 Dihedral : 18.690 86.041 6389 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.25 % Allowed : 30.27 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3636 helix: -0.01 (0.14), residues: 1258 sheet: -1.55 (0.21), residues: 562 loop : -1.64 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 294 HIS 0.021 0.001 HIS I 111 PHE 0.030 0.001 PHE F 411 TYR 0.035 0.001 TYR M 285 ARG 0.007 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1128) hydrogen bonds : angle 5.26174 ( 3145) covalent geometry : bond 0.00361 (35032) covalent geometry : angle 0.66171 (48160) *********************** 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 824 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 619 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2018 (tpp) cc_final: 0.1258 (tpt) REVERT: A 19 LYS cc_start: 0.8082 (mttt) cc_final: 0.7627 (mttp) REVERT: A 64 ILE cc_start: 0.6319 (tp) cc_final: 0.6072 (tp) REVERT: A 100 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: A 234 PHE cc_start: 0.6372 (m-10) cc_final: 0.6168 (m-10) REVERT: A 262 TYR cc_start: 0.8380 (t80) cc_final: 0.7951 (t80) REVERT: A 270 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6892 (ptmm) REVERT: A 447 LYS cc_start: 0.7884 (mptt) cc_final: 0.7660 (mptt) REVERT: A 458 ASP cc_start: 0.7513 (m-30) cc_final: 0.7007 (m-30) REVERT: B 14 ASP cc_start: 0.8674 (t0) cc_final: 0.8309 (t0) REVERT: B 83 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6454 (mtpt) REVERT: B 219 TRP cc_start: 0.6675 (m100) cc_final: 0.5575 (m100) REVERT: B 283 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7372 (mmm160) REVERT: B 352 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8677 (mmtm) REVERT: B 376 LYS cc_start: 0.7707 (mttm) cc_final: 0.7485 (mmmm) REVERT: B 409 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8211 (ptpp) REVERT: E 50 LEU cc_start: 0.7436 (mt) cc_final: 0.7168 (mt) REVERT: E 72 ARG cc_start: 0.7023 (mpp80) cc_final: 0.6654 (mmm160) REVERT: E 205 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6206 (tm-30) REVERT: E 227 SER cc_start: 0.6502 (p) cc_final: 0.6150 (p) REVERT: E 284 VAL cc_start: 0.4250 (OUTLIER) cc_final: 0.3827 (m) REVERT: E 296 ASN cc_start: 0.6083 (m-40) cc_final: 0.5670 (m-40) REVERT: E 364 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.5936 (mtm-85) REVERT: E 369 GLU cc_start: 0.7962 (pt0) cc_final: 0.7459 (pt0) REVERT: E 476 GLU cc_start: 0.7130 (pm20) cc_final: 0.6686 (pm20) REVERT: E 503 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.4063 (t80) REVERT: E 505 TYR cc_start: 0.6369 (m-80) cc_final: 0.6157 (m-80) REVERT: F 1 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (ptp) REVERT: F 13 GLU cc_start: 0.7394 (mp0) cc_final: 0.6657 (mp0) REVERT: F 52 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6309 (mt-10) REVERT: F 72 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5836 (tm-30) REVERT: F 89 GLN cc_start: 0.8284 (pm20) cc_final: 0.7957 (pm20) REVERT: F 135 PHE cc_start: 0.6013 (OUTLIER) cc_final: 0.5285 (t80) REVERT: F 157 ILE cc_start: 0.5043 (OUTLIER) cc_final: 0.4668 (tt) REVERT: F 169 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6282 (mm-30) REVERT: F 240 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7131 (mpp80) REVERT: F 324 SER cc_start: 0.8351 (t) cc_final: 0.7877 (p) REVERT: F 336 MET cc_start: 0.5562 (mpp) cc_final: 0.5258 (mpp) REVERT: I 35 GLN cc_start: 0.6877 (tp40) cc_final: 0.6541 (tp40) REVERT: I 85 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7088 (pptt) REVERT: I 406 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6404 (tpp) REVERT: I 429 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7144 (tt) REVERT: I 446 ASN cc_start: 0.5671 (OUTLIER) cc_final: 0.5008 (m110) REVERT: J 13 GLU cc_start: 0.8047 (mp0) cc_final: 0.7633 (mp0) REVERT: J 86 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8813 (mtmt) REVERT: J 159 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7693 (tt) REVERT: J 167 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.6140 (pttt) REVERT: J 171 TYR cc_start: 0.7732 (m-80) cc_final: 0.7348 (m-80) REVERT: J 181 PHE cc_start: 0.8431 (t80) cc_final: 0.8099 (t80) REVERT: J 211 LYS cc_start: 0.5978 (mttt) cc_final: 0.4761 (mmmt) REVERT: J 256 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.4359 (mt) REVERT: J 271 LYS cc_start: 0.9124 (tptt) cc_final: 0.8760 (tptt) REVERT: J 336 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.4595 (mpp) REVERT: J 362 ARG cc_start: 0.3621 (OUTLIER) cc_final: 0.2528 (mmp-170) REVERT: J 364 GLN cc_start: 0.4441 (mm-40) cc_final: 0.4224 (mm-40) REVERT: J 374 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7244 (ttt-90) REVERT: J 401 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7636 (tp) REVERT: M 52 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7732 (mm) REVERT: M 95 GLU cc_start: 0.7797 (tp30) cc_final: 0.7399 (tm-30) REVERT: M 106 PHE cc_start: 0.0843 (OUTLIER) cc_final: 0.0166 (m-80) REVERT: M 249 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7938 (mm-30) REVERT: M 262 TYR cc_start: 0.6589 (t80) cc_final: 0.6104 (t80) REVERT: M 355 LYS cc_start: 0.7237 (mtmt) cc_final: 0.6785 (tptm) REVERT: M 358 PHE cc_start: 0.7312 (m-10) cc_final: 0.6824 (m-10) REVERT: M 382 ASN cc_start: 0.7705 (m-40) cc_final: 0.7491 (m-40) REVERT: M 384 VAL cc_start: 0.8575 (t) cc_final: 0.7814 (m) REVERT: M 386 VAL cc_start: 0.8271 (t) cc_final: 0.7840 (m) REVERT: M 503 PHE cc_start: 0.5610 (t80) cc_final: 0.5305 (t80) REVERT: M 504 LYS cc_start: 0.4842 (OUTLIER) cc_final: 0.4399 (ptpp) REVERT: N 57 THR cc_start: 0.7729 (m) cc_final: 0.7409 (p) REVERT: N 181 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5619 (p90) REVERT: N 192 TRP cc_start: 0.7329 (p-90) cc_final: 0.6986 (p-90) REVERT: N 205 PHE cc_start: 0.7195 (t80) cc_final: 0.6817 (t80) REVERT: N 321 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7680 (t80) REVERT: N 409 LYS cc_start: 0.6640 (mttt) cc_final: 0.6370 (mmtp) REVERT: N 414 MET cc_start: 0.6978 (mmm) cc_final: 0.6535 (mmm) outliers start: 205 outliers final: 132 residues processed: 744 average time/residue: 0.6182 time to fit residues: 729.6033 Evaluate side-chains 739 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 582 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 216 THR 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 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain E residue 496 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 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 429 LEU 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 62 ILE Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR 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 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 336 MET 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 433 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE 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 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain M residue 504 LYS Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 58 CYS 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 106 ASP Chi-restraints excluded: chain N residue 108 ILE 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 258 ASN Chi-restraints excluded: chain N residue 271 LYS Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 199 optimal weight: 0.9980 chunk 335 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 292 optimal weight: 0.0670 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 261 optimal weight: 0.0470 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 111 HIS I 349 GLN ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 446 ASN N 69 ASN ** 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 = 0.4625 r_free = 0.4625 target = 0.181683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.149532 restraints weight = 69687.702| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 4.32 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35032 Z= 0.145 Angle : 0.666 14.666 48160 Z= 0.347 Chirality : 0.044 0.258 5276 Planarity : 0.005 0.100 5488 Dihedral : 18.669 86.347 6389 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 5.85 % Allowed : 30.88 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3636 helix: -0.00 (0.14), residues: 1256 sheet: -1.51 (0.20), residues: 590 loop : -1.65 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 231 HIS 0.025 0.001 HIS A 251 PHE 0.023 0.001 PHE N 45 TYR 0.026 0.001 TYR E 6 ARG 0.007 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1128) hydrogen bonds : angle 5.21282 ( 3145) covalent geometry : bond 0.00336 (35032) covalent geometry : angle 0.66566 (48160) *********************** 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 794 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 602 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8103 (mttt) cc_final: 0.7675 (mttp) REVERT: A 100 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6703 (pt0) REVERT: A 234 PHE cc_start: 0.6440 (m-10) cc_final: 0.6225 (m-10) REVERT: A 262 TYR cc_start: 0.8379 (t80) cc_final: 0.7884 (t80) REVERT: A 406 MET cc_start: 0.7242 (tmm) cc_final: 0.6911 (tmm) REVERT: A 458 ASP cc_start: 0.7514 (m-30) cc_final: 0.7002 (m-30) REVERT: B 14 ASP cc_start: 0.8733 (t0) cc_final: 0.8316 (t0) REVERT: B 219 TRP cc_start: 0.6802 (m100) cc_final: 0.5695 (m100) REVERT: B 283 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7412 (mmm160) REVERT: B 352 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8691 (mmtm) REVERT: E 72 ARG cc_start: 0.7054 (mpp80) cc_final: 0.6720 (mmm160) REVERT: E 205 GLN cc_start: 0.6688 (tm-30) cc_final: 0.6264 (tm-30) REVERT: E 227 SER cc_start: 0.6539 (p) cc_final: 0.6182 (p) REVERT: E 363 THR cc_start: 0.7053 (t) cc_final: 0.5634 (m) REVERT: E 364 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.5754 (mtm-85) REVERT: E 369 GLU cc_start: 0.7943 (pt0) cc_final: 0.7419 (pt0) REVERT: E 476 GLU cc_start: 0.7075 (pm20) cc_final: 0.6625 (pm20) REVERT: E 503 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.4037 (t80) REVERT: F 52 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6443 (mt-10) REVERT: F 72 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5788 (tm-30) REVERT: F 89 GLN cc_start: 0.8303 (pm20) cc_final: 0.7962 (pm20) REVERT: F 111 GLU cc_start: 0.7884 (tp30) cc_final: 0.7651 (tp30) REVERT: F 135 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5177 (t80) REVERT: F 157 ILE cc_start: 0.5016 (tp) cc_final: 0.4698 (tt) REVERT: F 169 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6307 (mm-30) REVERT: F 240 ARG cc_start: 0.7435 (mtm-85) cc_final: 0.7212 (mpp80) REVERT: F 304 LYS cc_start: 0.8872 (tppt) cc_final: 0.8251 (mmmm) REVERT: F 324 SER cc_start: 0.8401 (t) cc_final: 0.7876 (p) REVERT: I 8 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: I 35 GLN cc_start: 0.6925 (tp40) cc_final: 0.6581 (tp40) REVERT: I 74 MET cc_start: 0.3134 (pmm) cc_final: 0.2777 (pmm) REVERT: I 85 LYS cc_start: 0.7456 (pttt) cc_final: 0.7087 (pptt) REVERT: I 406 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6377 (tpp) REVERT: I 429 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7109 (tt) REVERT: I 446 ASN cc_start: 0.5652 (OUTLIER) cc_final: 0.5113 (m110) REVERT: J 13 GLU cc_start: 0.8066 (mp0) cc_final: 0.7550 (mp0) REVERT: J 86 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8708 (mtpt) REVERT: J 159 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7669 (tt) REVERT: J 181 PHE cc_start: 0.8445 (t80) cc_final: 0.8093 (t80) REVERT: J 211 LYS cc_start: 0.5928 (mttt) cc_final: 0.4755 (mmmt) REVERT: J 256 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.4421 (mt) REVERT: J 271 LYS cc_start: 0.9128 (tptt) cc_final: 0.8874 (tptt) REVERT: J 274 GLU cc_start: 0.8586 (pp20) cc_final: 0.8251 (pp20) REVERT: J 294 TRP cc_start: 0.6339 (p-90) cc_final: 0.5518 (p-90) REVERT: J 336 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.4512 (mpp) REVERT: J 362 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.2527 (mmp-170) REVERT: J 401 ILE cc_start: 0.7860 (mm) cc_final: 0.7608 (tp) REVERT: M 52 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7697 (mm) REVERT: M 95 GLU cc_start: 0.7746 (tp30) cc_final: 0.7343 (tm-30) REVERT: M 106 PHE cc_start: 0.0693 (OUTLIER) cc_final: -0.0007 (m-80) REVERT: M 249 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7941 (mp0) REVERT: M 355 LYS cc_start: 0.7223 (mtmt) cc_final: 0.6801 (tptm) REVERT: M 358 PHE cc_start: 0.7333 (m-10) cc_final: 0.6814 (m-10) REVERT: M 382 ASN cc_start: 0.7828 (m-40) cc_final: 0.7598 (m-40) REVERT: M 384 VAL cc_start: 0.8551 (t) cc_final: 0.7795 (m) REVERT: M 386 VAL cc_start: 0.8209 (t) cc_final: 0.7768 (m) REVERT: N 14 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: N 92 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7659 (tpp) REVERT: N 152 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8322 (tp) REVERT: N 181 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5558 (p90) REVERT: N 192 TRP cc_start: 0.7337 (p-90) cc_final: 0.7086 (p-90) REVERT: N 205 PHE cc_start: 0.7322 (t80) cc_final: 0.6857 (t80) REVERT: N 321 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7692 (t80) REVERT: N 361 ARG cc_start: 0.6571 (tpt90) cc_final: 0.6320 (tpt90) REVERT: N 409 LYS cc_start: 0.6637 (mttt) cc_final: 0.6365 (mmtp) REVERT: N 414 MET cc_start: 0.6824 (mmm) cc_final: 0.6358 (mmm) outliers start: 192 outliers final: 138 residues processed: 732 average time/residue: 0.4702 time to fit residues: 547.9965 Evaluate side-chains 738 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 580 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 216 THR 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 282 VAL 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 392 TYR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain E residue 496 ILE Chi-restraints excluded: chain E residue 503 PHE 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 135 PHE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 41 SER 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 271 LEU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 429 LEU 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 11 THR 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 132 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 THR 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 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 336 MET 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 372 LYS 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 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE 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 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 14 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 58 CYS Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 106 ASP 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 258 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 305 optimal weight: 0.0020 chunk 309 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 268 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 333 optimal weight: 2.9990 chunk 344 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN I 111 HIS ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** 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 446 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.181236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.148793 restraints weight = 70714.583| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 4.40 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35032 Z= 0.150 Angle : 0.685 15.037 48160 Z= 0.355 Chirality : 0.045 0.276 5276 Planarity : 0.005 0.125 5488 Dihedral : 18.648 86.288 6389 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.64 % Allowed : 31.55 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3636 helix: -0.03 (0.14), residues: 1282 sheet: -1.53 (0.20), residues: 590 loop : -1.61 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 294 HIS 0.022 0.001 HIS A 251 PHE 0.033 0.001 PHE M 503 TYR 0.030 0.001 TYR F 233 ARG 0.009 0.001 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 1128) hydrogen bonds : angle 5.19725 ( 3145) covalent geometry : bond 0.00350 (35032) covalent geometry : angle 0.68528 (48160) *********************** 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 783 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 598 time to evaluate : 3.547 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: 0.8092 (mttt) cc_final: 0.7672 (mttp) REVERT: A 234 PHE cc_start: 0.6499 (m-10) cc_final: 0.6293 (m-10) REVERT: A 262 TYR cc_start: 0.8346 (t80) cc_final: 0.7956 (t80) REVERT: A 356 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 458 ASP cc_start: 0.7540 (m-30) cc_final: 0.7029 (m-30) REVERT: B 14 ASP cc_start: 0.8729 (t0) cc_final: 0.8282 (t0) REVERT: B 219 TRP cc_start: 0.6801 (m100) cc_final: 0.5726 (m100) REVERT: B 262 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: B 283 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7519 (mmm160) REVERT: B 304 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8453 (mmmt) REVERT: B 352 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8741 (mmtm) REVERT: B 361 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6838 (ttp-110) REVERT: B 366 LYS cc_start: 0.6844 (mtmt) cc_final: 0.6614 (ptpt) REVERT: E 205 GLN cc_start: 0.6849 (tm-30) cc_final: 0.6473 (tm-30) REVERT: E 227 SER cc_start: 0.6538 (p) cc_final: 0.6183 (p) REVERT: E 249 GLU cc_start: 0.7499 (tp30) cc_final: 0.7015 (tp30) REVERT: E 363 THR cc_start: 0.7081 (t) cc_final: 0.5647 (m) REVERT: E 364 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.5696 (mtm-85) REVERT: E 369 GLU cc_start: 0.8025 (pt0) cc_final: 0.7519 (pt0) REVERT: E 476 GLU cc_start: 0.7013 (pm20) cc_final: 0.6553 (pm20) REVERT: E 503 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.4024 (t80) REVERT: F 13 GLU cc_start: 0.7623 (mp0) cc_final: 0.7264 (mp0) REVERT: F 52 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6444 (mt-10) REVERT: F 72 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5796 (tm-30) REVERT: F 89 GLN cc_start: 0.8328 (pm20) cc_final: 0.7971 (pm20) REVERT: F 111 GLU cc_start: 0.7993 (tp30) cc_final: 0.7758 (tp30) REVERT: F 135 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.5363 (t80) REVERT: F 157 ILE cc_start: 0.4832 (tp) cc_final: 0.4623 (tp) REVERT: F 169 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6333 (mm-30) REVERT: F 240 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7243 (mpp80) REVERT: F 304 LYS cc_start: 0.8839 (tppt) cc_final: 0.8204 (mmmm) REVERT: F 324 SER cc_start: 0.8345 (t) cc_final: 0.7819 (p) REVERT: I 8 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: I 35 GLN cc_start: 0.6955 (tp40) cc_final: 0.6609 (tp40) REVERT: I 74 MET cc_start: 0.3129 (pmm) cc_final: 0.2894 (pmm) REVERT: I 85 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7181 (pptt) REVERT: I 132 ASP cc_start: 0.6551 (t0) cc_final: 0.6308 (m-30) REVERT: I 284 VAL cc_start: 0.5333 (OUTLIER) cc_final: 0.4797 (m) REVERT: I 398 LYS cc_start: 0.7570 (tptt) cc_final: 0.6920 (tptt) REVERT: I 406 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6301 (tpp) REVERT: I 429 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7113 (tt) REVERT: I 446 ASN cc_start: 0.5621 (OUTLIER) cc_final: 0.5120 (m110) REVERT: J 13 GLU cc_start: 0.8010 (mp0) cc_final: 0.7513 (mp0) REVERT: J 159 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7680 (tt) REVERT: J 181 PHE cc_start: 0.8518 (t80) cc_final: 0.8134 (t80) REVERT: J 211 LYS cc_start: 0.5926 (mttt) cc_final: 0.4707 (mmmt) REVERT: J 256 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.4617 (mt) REVERT: J 271 LYS cc_start: 0.9204 (tptt) cc_final: 0.8878 (tptt) REVERT: J 274 GLU cc_start: 0.8656 (pp20) cc_final: 0.8406 (pp20) REVERT: J 283 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.4574 (ptt90) REVERT: J 336 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.4517 (mpp) REVERT: J 362 ARG cc_start: 0.3486 (OUTLIER) cc_final: 0.2439 (mmp-170) REVERT: M 52 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7686 (mm) REVERT: M 95 GLU cc_start: 0.7727 (tp30) cc_final: 0.7338 (tm-30) REVERT: M 106 PHE cc_start: 0.0731 (OUTLIER) cc_final: 0.0150 (m-80) REVERT: M 249 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7988 (mp0) REVERT: M 355 LYS cc_start: 0.7272 (mtmt) cc_final: 0.6893 (tptm) REVERT: M 358 PHE cc_start: 0.7364 (m-10) cc_final: 0.6844 (m-10) REVERT: M 382 ASN cc_start: 0.7768 (m-40) cc_final: 0.7561 (m-40) REVERT: M 384 VAL cc_start: 0.8548 (t) cc_final: 0.7784 (m) REVERT: M 386 VAL cc_start: 0.8194 (t) cc_final: 0.7768 (m) REVERT: N 14 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: N 92 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7649 (tpp) REVERT: N 181 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.5686 (p90) REVERT: N 192 TRP cc_start: 0.7324 (p-90) cc_final: 0.7099 (p-90) REVERT: N 205 PHE cc_start: 0.7335 (t80) cc_final: 0.6873 (t80) REVERT: N 321 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7704 (t80) REVERT: N 409 LYS cc_start: 0.6622 (mttt) cc_final: 0.6343 (mmtp) outliers start: 185 outliers final: 131 residues processed: 722 average time/residue: 0.4859 time to fit residues: 561.2409 Evaluate side-chains 727 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 573 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 116 ASP 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 251 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 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 216 THR 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 334 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 295 GLN Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain E residue 503 PHE 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 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 429 LEU 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 11 THR 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 132 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR 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 283 ARG Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 336 MET 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 372 LYS 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 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE 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 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 14 ASP Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 58 CYS Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 ILE 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 234 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 182 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 257 optimal weight: 7.9990 chunk 151 optimal weight: 0.0070 chunk 345 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 183 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** M 35 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.182257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.150609 restraints weight = 69606.287| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 4.16 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35032 Z= 0.143 Angle : 0.698 16.259 48160 Z= 0.360 Chirality : 0.044 0.220 5276 Planarity : 0.005 0.105 5488 Dihedral : 18.638 86.981 6389 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.88 % Allowed : 32.53 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3636 helix: -0.05 (0.14), residues: 1288 sheet: -1.49 (0.21), residues: 576 loop : -1.62 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 231 HIS 0.029 0.001 HIS A 251 PHE 0.024 0.001 PHE M 82 TYR 0.025 0.001 TYR B 105 ARG 0.014 0.001 ARG J 374 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 1128) hydrogen bonds : angle 5.18156 ( 3145) covalent geometry : bond 0.00334 (35032) covalent geometry : angle 0.69775 (48160) *********************** 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 753 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 593 time to evaluate : 3.623 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: 0.8148 (mttt) cc_final: 0.7732 (mttp) REVERT: A 100 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6814 (pt0) REVERT: A 234 PHE cc_start: 0.6490 (m-10) cc_final: 0.6283 (m-10) REVERT: A 262 TYR cc_start: 0.8318 (t80) cc_final: 0.7867 (t80) REVERT: A 406 MET cc_start: 0.7226 (tmm) cc_final: 0.6968 (tmm) REVERT: A 458 ASP cc_start: 0.7528 (m-30) cc_final: 0.7010 (m-30) REVERT: A 485 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6370 (mttt) REVERT: B 14 ASP cc_start: 0.8757 (t0) cc_final: 0.8300 (t0) REVERT: B 83 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6349 (mtpt) REVERT: B 196 LYS cc_start: 0.8338 (tppt) cc_final: 0.7987 (tppt) REVERT: B 219 TRP cc_start: 0.6698 (m100) cc_final: 0.5938 (m100) REVERT: B 262 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: B 279 ASP cc_start: 0.8009 (m-30) cc_final: 0.7635 (m-30) REVERT: B 283 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7391 (mmm160) REVERT: B 302 LYS cc_start: 0.8589 (tppt) cc_final: 0.8279 (mtmm) REVERT: B 352 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8711 (mmtm) REVERT: B 361 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6863 (ttp-110) REVERT: B 366 LYS cc_start: 0.6819 (mtmt) cc_final: 0.6530 (ptpt) REVERT: E 205 GLN cc_start: 0.6722 (tm-30) cc_final: 0.6120 (tm-30) REVERT: E 227 SER cc_start: 0.6899 (p) cc_final: 0.6505 (p) REVERT: E 263 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8151 (mmtt) REVERT: E 364 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.5750 (mtm-85) REVERT: E 369 GLU cc_start: 0.7985 (pt0) cc_final: 0.7495 (pt0) REVERT: E 406 MET cc_start: 0.7426 (ptp) cc_final: 0.7186 (ptp) REVERT: E 476 GLU cc_start: 0.6970 (pm20) cc_final: 0.6607 (pm20) REVERT: E 503 PHE cc_start: 0.5828 (OUTLIER) cc_final: 0.4058 (t80) REVERT: F 13 GLU cc_start: 0.7579 (mp0) cc_final: 0.7171 (mp0) REVERT: F 52 GLU cc_start: 0.6566 (mt-10) cc_final: 0.6233 (mt-10) REVERT: F 72 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5741 (tm-30) REVERT: F 89 GLN cc_start: 0.8281 (pm20) cc_final: 0.7919 (pm20) REVERT: F 135 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5311 (t80) REVERT: F 157 ILE cc_start: 0.4774 (tp) cc_final: 0.4555 (tp) REVERT: F 169 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6304 (mm-30) REVERT: F 240 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7267 (mpp80) REVERT: F 289 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8736 (mmtm) REVERT: F 304 LYS cc_start: 0.8830 (tppt) cc_final: 0.8228 (mmmm) REVERT: F 324 SER cc_start: 0.8335 (t) cc_final: 0.7796 (p) REVERT: I 8 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: I 35 GLN cc_start: 0.6938 (tp40) cc_final: 0.6585 (tp40) REVERT: I 74 MET cc_start: 0.3038 (pmm) cc_final: 0.2823 (pmm) REVERT: I 85 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7170 (pptt) REVERT: I 132 ASP cc_start: 0.6502 (t0) cc_final: 0.6197 (m-30) REVERT: I 267 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8215 (mtmm) REVERT: I 284 VAL cc_start: 0.5323 (OUTLIER) cc_final: 0.4778 (m) REVERT: I 406 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6322 (tpp) REVERT: I 429 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7041 (tt) REVERT: I 446 ASN cc_start: 0.5479 (OUTLIER) cc_final: 0.4945 (m110) REVERT: I 476 GLU cc_start: 0.7257 (pm20) cc_final: 0.7006 (pm20) REVERT: J 13 GLU cc_start: 0.7988 (mp0) cc_final: 0.7507 (mp0) REVERT: J 122 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8621 (mmmt) REVERT: J 159 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7707 (tt) REVERT: J 181 PHE cc_start: 0.8524 (t80) cc_final: 0.8172 (t80) REVERT: J 256 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.4748 (mt) REVERT: J 271 LYS cc_start: 0.9178 (tptt) cc_final: 0.8848 (tptt) REVERT: J 283 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4589 (ptt90) REVERT: J 336 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.4559 (mpp) REVERT: J 345 MET cc_start: 0.8258 (tmm) cc_final: 0.7791 (tmm) REVERT: J 362 ARG cc_start: 0.3452 (OUTLIER) cc_final: 0.2448 (mmp-170) REVERT: M 52 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7696 (mm) REVERT: M 95 GLU cc_start: 0.7660 (tp30) cc_final: 0.7297 (tm-30) REVERT: M 133 GLU cc_start: 0.5772 (mm-30) cc_final: 0.5284 (mm-30) REVERT: M 249 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8053 (mp0) REVERT: M 355 LYS cc_start: 0.7223 (mtmt) cc_final: 0.6903 (tptm) REVERT: M 358 PHE cc_start: 0.7399 (m-10) cc_final: 0.6918 (m-10) REVERT: M 382 ASN cc_start: 0.7788 (m-40) cc_final: 0.7584 (m-40) REVERT: M 384 VAL cc_start: 0.8543 (t) cc_final: 0.7893 (m) REVERT: M 386 VAL cc_start: 0.8176 (t) cc_final: 0.7742 (m) REVERT: N 92 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7631 (tpp) REVERT: N 181 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.5345 (p90) REVERT: N 205 PHE cc_start: 0.7258 (t80) cc_final: 0.6815 (t80) REVERT: N 277 MET cc_start: 0.6147 (ttt) cc_final: 0.5335 (mmt) REVERT: N 321 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7690 (t80) REVERT: N 374 ARG cc_start: 0.7506 (ptm-80) cc_final: 0.7281 (ptm-80) REVERT: N 409 LYS cc_start: 0.6592 (mttt) cc_final: 0.6313 (mmtp) outliers start: 160 outliers final: 121 residues processed: 699 average time/residue: 0.5037 time to fit residues: 561.0591 Evaluate side-chains 722 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 576 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLU 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 251 HIS 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 442 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 216 THR 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 334 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 429 LEU 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 11 THR 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 132 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 336 MET 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 372 LYS Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 55 SER 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 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 58 CYS Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 ILE 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 234 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 368 TRP Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 240 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 188 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS J 364 GLN ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.180473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.148065 restraints weight = 70697.219| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 4.35 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35032 Z= 0.157 Angle : 0.717 15.796 48160 Z= 0.369 Chirality : 0.045 0.236 5276 Planarity : 0.005 0.092 5488 Dihedral : 18.638 89.702 6389 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.73 % Allowed : 32.74 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3636 helix: -0.06 (0.14), residues: 1284 sheet: -1.55 (0.21), residues: 580 loop : -1.63 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 231 HIS 0.033 0.001 HIS A 251 PHE 0.048 0.001 PHE M 503 TYR 0.027 0.001 TYR F 233 ARG 0.013 0.001 ARG J 374 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 1128) hydrogen bonds : angle 5.21217 ( 3145) covalent geometry : bond 0.00368 (35032) covalent geometry : angle 0.71725 (48160) ********************** 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 749 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 594 time to evaluate : 3.434 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: 0.8164 (mttt) cc_final: 0.7758 (mttp) REVERT: A 100 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: A 234 PHE cc_start: 0.6576 (m-10) cc_final: 0.6354 (m-10) REVERT: A 262 TYR cc_start: 0.8353 (t80) cc_final: 0.7960 (t80) REVERT: A 406 MET cc_start: 0.7297 (tmm) cc_final: 0.7019 (tmm) REVERT: A 458 ASP cc_start: 0.7548 (m-30) cc_final: 0.7014 (m-30) REVERT: A 485 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6378 (mttt) REVERT: B 14 ASP cc_start: 0.8734 (t0) cc_final: 0.8317 (t0) REVERT: B 83 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6348 (mtpt) REVERT: B 105 TYR cc_start: 0.7381 (t80) cc_final: 0.7058 (t80) REVERT: B 219 TRP cc_start: 0.6708 (m100) cc_final: 0.5834 (m100) REVERT: B 262 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: B 279 ASP cc_start: 0.8092 (m-30) cc_final: 0.7710 (m-30) REVERT: B 283 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7625 (mmm160) REVERT: B 302 LYS cc_start: 0.8452 (tppt) cc_final: 0.8075 (mtmm) REVERT: B 352 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8745 (mmtm) REVERT: B 361 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6889 (ttp-110) REVERT: B 366 LYS cc_start: 0.6945 (mtmt) cc_final: 0.6665 (ptpt) REVERT: E 85 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7360 (pttm) REVERT: E 205 GLN cc_start: 0.6784 (tm-30) cc_final: 0.6163 (tm-30) REVERT: E 227 SER cc_start: 0.7164 (p) cc_final: 0.6783 (p) REVERT: E 249 GLU cc_start: 0.7525 (tp30) cc_final: 0.7143 (tp30) REVERT: E 369 GLU cc_start: 0.8008 (pt0) cc_final: 0.7585 (pt0) REVERT: E 406 MET cc_start: 0.7396 (ptp) cc_final: 0.7133 (ptp) REVERT: E 476 GLU cc_start: 0.6963 (pm20) cc_final: 0.6618 (pm20) REVERT: E 503 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4115 (t80) REVERT: F 13 GLU cc_start: 0.7633 (mp0) cc_final: 0.7218 (mp0) REVERT: F 52 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6443 (mt-10) REVERT: F 72 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5861 (tm-30) REVERT: F 135 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5407 (t80) REVERT: F 157 ILE cc_start: 0.4776 (tp) cc_final: 0.4505 (tp) REVERT: F 169 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6416 (mm-30) REVERT: F 198 PHE cc_start: 0.7247 (t80) cc_final: 0.6423 (t80) REVERT: F 289 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8811 (mmtm) REVERT: F 304 LYS cc_start: 0.8811 (tppt) cc_final: 0.8204 (mmmm) REVERT: F 324 SER cc_start: 0.8330 (t) cc_final: 0.7813 (p) REVERT: I 8 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: I 35 GLN cc_start: 0.6965 (tp40) cc_final: 0.6597 (tp40) REVERT: I 74 MET cc_start: 0.3034 (pmm) cc_final: 0.2823 (pmm) REVERT: I 85 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7240 (pptt) REVERT: I 132 ASP cc_start: 0.6539 (t0) cc_final: 0.6205 (m-30) REVERT: I 267 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8227 (mtmm) REVERT: I 313 PHE cc_start: 0.3306 (OUTLIER) cc_final: 0.3045 (m-80) REVERT: I 406 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6267 (tpp) REVERT: I 429 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6992 (tt) REVERT: I 446 ASN cc_start: 0.5577 (OUTLIER) cc_final: 0.5030 (m110) REVERT: I 497 LYS cc_start: 0.8016 (tppt) cc_final: 0.7808 (tppt) REVERT: J 13 GLU cc_start: 0.8000 (mp0) cc_final: 0.7529 (mp0) REVERT: J 159 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7720 (tt) REVERT: J 181 PHE cc_start: 0.8519 (t80) cc_final: 0.8157 (t80) REVERT: J 256 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.4879 (mt) REVERT: J 271 LYS cc_start: 0.9182 (tptt) cc_final: 0.8828 (tptt) REVERT: J 283 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.4635 (ptt90) REVERT: J 336 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.4514 (mpp) REVERT: J 345 MET cc_start: 0.8367 (tmm) cc_final: 0.7956 (tmm) REVERT: J 362 ARG cc_start: 0.3527 (OUTLIER) cc_final: 0.2361 (mmp-170) REVERT: M 52 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7721 (mm) REVERT: M 95 GLU cc_start: 0.7662 (tp30) cc_final: 0.7289 (tm-30) REVERT: M 106 PHE cc_start: 0.0727 (OUTLIER) cc_final: 0.0139 (m-80) REVERT: M 133 GLU cc_start: 0.5836 (mm-30) cc_final: 0.5321 (mm-30) REVERT: M 249 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8021 (mp0) REVERT: M 355 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6919 (tptm) REVERT: M 358 PHE cc_start: 0.7396 (m-10) cc_final: 0.6902 (m-10) REVERT: M 382 ASN cc_start: 0.7857 (m-40) cc_final: 0.7657 (m-40) REVERT: M 384 VAL cc_start: 0.8546 (t) cc_final: 0.7869 (m) REVERT: M 386 VAL cc_start: 0.8191 (t) cc_final: 0.7777 (m) REVERT: N 92 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7577 (tpp) REVERT: N 181 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5534 (p90) REVERT: N 205 PHE cc_start: 0.7244 (t80) cc_final: 0.6773 (t80) REVERT: N 321 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7725 (t80) REVERT: N 409 LYS cc_start: 0.6603 (mttt) cc_final: 0.6318 (mmtp) outliers start: 155 outliers final: 118 residues processed: 702 average time/residue: 0.5623 time to fit residues: 639.0300 Evaluate side-chains 721 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 577 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 116 ASP 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 251 HIS 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 442 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 216 THR 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 334 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 445 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 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 259 TYR Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 375 GLU Chi-restraints excluded: chain F residue 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 I residue 3 GLU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 271 LEU Chi-restraints excluded: chain I residue 313 PHE Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 429 LEU 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 11 THR 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 132 LEU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 336 MET 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 372 LYS Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE 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 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 58 CYS Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 ILE 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 234 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 304 LYS Chi-restraints excluded: chain N residue 320 HIS Chi-restraints excluded: chain N residue 321 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 371 ASP Chi-restraints excluded: chain N residue 387 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 122 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 271 optimal weight: 0.0970 chunk 356 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS F 267 GLN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 HIS ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.179531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.148317 restraints weight = 71337.135| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 4.02 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35032 Z= 0.158 Angle : 0.725 16.166 48160 Z= 0.373 Chirality : 0.045 0.345 5276 Planarity : 0.005 0.084 5488 Dihedral : 18.649 88.032 6389 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.82 % Allowed : 33.05 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3636 helix: -0.07 (0.14), residues: 1284 sheet: -1.58 (0.20), residues: 604 loop : -1.60 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 231 HIS 0.015 0.001 HIS A 251 PHE 0.040 0.001 PHE M 503 TYR 0.044 0.001 TYR I 104 ARG 0.011 0.001 ARG J 374 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 1128) hydrogen bonds : angle 5.23253 ( 3145) covalent geometry : bond 0.00371 (35032) covalent geometry : angle 0.72495 (48160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17700.28 seconds wall clock time: 315 minutes 10.24 seconds (18910.24 seconds total)