Starting phenix.real_space_refine on Thu Feb 22 09:56:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it1_35703/02_2024/8it1_35703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it1_35703/02_2024/8it1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it1_35703/02_2024/8it1_35703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it1_35703/02_2024/8it1_35703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it1_35703/02_2024/8it1_35703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8it1_35703/02_2024/8it1_35703.pdb" } 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 Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "I GLU 488": "OE1" <-> "OE2" Residue "J GLU 441": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "N TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.64, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.81 Conformation dependent library (CDL) restraints added in 5.0 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: 11.16 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: 11.93 Time building geometry restraints manager: 14.60 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: 93.97 - 102.36: 319 102.36 - 110.75: 12337 110.75 - 119.14: 17100 119.14 - 127.52: 17807 127.52 - 135.91: 597 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 2.440 nonbonded pdb=" OD1 ASN I 90 " pdb=" OH TYR M 37 " model vdw 2.227 2.440 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 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 16.370 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 90.260 Find NCS groups from input model: 2.350 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.180 ------------------------------------------------------------------------------- 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= 0.303 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 770 time to evaluate : 3.521 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: 0.5300 time to fit residues: 642.1641 Evaluate side-chains 591 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 590 time to evaluate : 3.517 ------------------------------------------------------------------------------- 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: 6.9990 chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 2.9990 chunk 153 optimal weight: 0.0470 chunk 297 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 221 optimal weight: 0.1980 chunk 345 optimal weight: 0.8980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 251 HIS A 341 GLN A 466 ASN B 349 ASN E 90 ASN E 122 ASN E 374 ASN F 340 HIS I 111 HIS I 201 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN ** J 357 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 307 ASN ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 454 GLN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN N 258 ASN N 320 HIS ** N 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.1804 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= 0.193 Angle : 0.616 13.548 48160 Z= 0.326 Chirality : 0.043 0.336 5276 Planarity : 0.005 0.062 5488 Dihedral : 18.538 82.039 6389 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.69 % Allowed : 30.79 % Favored : 65.52 % 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: -1.69 (0.13), residues: 3636 helix: -0.21 (0.14), residues: 1313 sheet: -1.27 (0.23), residues: 490 loop : -1.75 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 294 HIS 0.012 0.001 HIS I 111 PHE 0.023 0.001 PHE N 411 TYR 0.020 0.001 TYR E 346 ARG 0.008 0.001 ARG M 24 *********************** 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 776 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 655 time to evaluate : 3.494 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: A 64 ILE cc_start: 0.6377 (tp) cc_final: 0.6160 (tp) REVERT: A 251 HIS cc_start: 0.4835 (OUTLIER) cc_final: 0.4457 (m90) REVERT: A 262 TYR cc_start: 0.7448 (t80) cc_final: 0.6989 (t80) REVERT: B 14 ASP cc_start: 0.7561 (t0) cc_final: 0.7299 (t0) REVERT: B 37 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7378 (pp) REVERT: B 222 ASP cc_start: 0.5986 (p0) cc_final: 0.5771 (p0) REVERT: E 117 LEU cc_start: 0.7140 (tp) cc_final: 0.6814 (tt) REVERT: F 135 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5511 (t80) REVERT: F 277 MET cc_start: 0.5324 (tmm) cc_final: 0.5119 (tmm) REVERT: F 398 GLU cc_start: 0.6236 (pp20) cc_final: 0.5960 (pp20) REVERT: I 248 ILE cc_start: 0.7504 (pt) cc_final: 0.7070 (pt) REVERT: I 474 ASP cc_start: 0.2968 (t0) cc_final: 0.2675 (t0) REVERT: J 57 THR cc_start: 0.7824 (m) cc_final: 0.7597 (m) REVERT: J 433 ILE cc_start: 0.7172 (pt) cc_final: 0.6845 (mt) REVERT: M 384 VAL cc_start: 0.8248 (t) cc_final: 0.8017 (m) REVERT: M 474 ASP cc_start: 0.5348 (t0) cc_final: 0.4614 (t0) REVERT: M 481 ARG cc_start: 0.6562 (tpp80) cc_final: 0.6147 (ttt180) REVERT: N 158 PHE cc_start: 0.4906 (t80) cc_final: 0.4656 (t80) outliers start: 121 outliers final: 58 residues processed: 724 average time/residue: 0.4933 time to fit residues: 569.6540 Evaluate side-chains 654 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 593 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 290 THR 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 203 ASP 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 1 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 208 ILE 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 410 PHE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 328 LYS Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 258 ASN 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 191 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 287 optimal weight: 0.4980 chunk 234 optimal weight: 0.0270 chunk 95 optimal weight: 4.9990 chunk 345 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 chunk 307 optimal weight: 0.2980 chunk 342 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 overall best weight: 0.3840 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS I 201 ASN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 446 ASN J 69 ASN J 314 GLN ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 GLN ** N 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35032 Z= 0.183 Angle : 0.597 12.457 48160 Z= 0.315 Chirality : 0.042 0.284 5276 Planarity : 0.004 0.060 5488 Dihedral : 18.526 83.468 6388 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.66 % Allowed : 30.67 % Favored : 64.66 % 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: -1.55 (0.13), residues: 3636 helix: 0.00 (0.14), residues: 1301 sheet: -1.33 (0.23), residues: 487 loop : -1.70 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 294 HIS 0.028 0.001 HIS A 251 PHE 0.022 0.001 PHE M 503 TYR 0.030 0.001 TYR I 397 ARG 0.006 0.000 ARG M 364 *********************** 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 777 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 624 time to evaluate : 3.414 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: A 262 TYR cc_start: 0.7502 (t80) cc_final: 0.6975 (t80) REVERT: B 14 ASP cc_start: 0.7631 (t0) cc_final: 0.7403 (t0) REVERT: B 222 ASP cc_start: 0.6158 (p0) cc_final: 0.5929 (p0) REVERT: E 117 LEU cc_start: 0.7152 (tp) cc_final: 0.6731 (tt) REVERT: F 135 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5266 (t80) REVERT: F 161 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5607 (m-30) REVERT: F 178 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5370 (mp) REVERT: I 35 GLN cc_start: 0.6728 (tp40) cc_final: 0.6270 (tp40) REVERT: I 303 MET cc_start: 0.8067 (tmm) cc_final: 0.7721 (tmm) REVERT: I 488 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: J 57 THR cc_start: 0.7840 (m) cc_final: 0.7616 (m) REVERT: J 138 GLN cc_start: 0.7711 (mp10) cc_final: 0.7399 (mp10) REVERT: M 106 PHE cc_start: 0.2387 (OUTLIER) cc_final: 0.1745 (m-80) REVERT: M 363 THR cc_start: 0.7250 (t) cc_final: 0.6981 (p) REVERT: M 386 VAL cc_start: 0.7900 (t) cc_final: 0.7635 (m) REVERT: M 474 ASP cc_start: 0.5191 (t0) cc_final: 0.4486 (t0) REVERT: M 481 ARG cc_start: 0.6704 (tpp80) cc_final: 0.6289 (ttt180) REVERT: N 2 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7559 (ptp-170) REVERT: N 44 ASP cc_start: 0.5922 (OUTLIER) cc_final: 0.5680 (m-30) REVERT: N 158 PHE cc_start: 0.4967 (t80) cc_final: 0.4715 (t80) REVERT: N 414 MET cc_start: 0.6949 (mmm) cc_final: 0.6562 (mmm) outliers start: 153 outliers final: 85 residues processed: 713 average time/residue: 0.4732 time to fit residues: 537.9961 Evaluate side-chains 677 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 585 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 285 TYR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 290 THR 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 368 TRP Chi-restraints excluded: chain B residue 372 LYS 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 155 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 221 THR 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 1 MET Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 178 ILE 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 280 LYS 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 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 320 HIS Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 370 ASN 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 106 PHE Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain M residue 307 ASN Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 496 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 164 optimal weight: 0.5980 chunk 232 optimal weight: 0.6980 chunk 346 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 181 optimal weight: 0.0470 chunk 328 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 129 ASN F 188 HIS I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 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 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN N 405 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35032 Z= 0.183 Angle : 0.602 14.421 48160 Z= 0.314 Chirality : 0.042 0.344 5276 Planarity : 0.004 0.063 5488 Dihedral : 18.524 84.693 6388 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.27 % Allowed : 31.07 % Favored : 63.66 % 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: -1.41 (0.13), residues: 3636 helix: 0.19 (0.14), residues: 1273 sheet: -1.31 (0.23), residues: 484 loop : -1.65 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 294 HIS 0.009 0.001 HIS I 207 PHE 0.028 0.001 PHE N 411 TYR 0.024 0.001 TYR M 285 ARG 0.006 0.000 ARG N 361 *********************** 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 796 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 623 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8022 (pt) cc_final: 0.7797 (pt) REVERT: A 251 HIS cc_start: 0.4769 (OUTLIER) cc_final: 0.4403 (m90) REVERT: A 262 TYR cc_start: 0.7525 (t80) cc_final: 0.6985 (t80) REVERT: B 14 ASP cc_start: 0.7737 (t0) cc_final: 0.7525 (t0) REVERT: B 222 ASP cc_start: 0.6125 (p0) cc_final: 0.5908 (p0) REVERT: E 137 ASP cc_start: 0.6888 (m-30) cc_final: 0.6512 (m-30) REVERT: F 135 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5227 (t80) REVERT: F 161 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5659 (m-30) REVERT: F 336 MET cc_start: 0.6131 (mpp) cc_final: 0.5574 (mpp) REVERT: I 35 GLN cc_start: 0.6751 (tp40) cc_final: 0.6282 (tp40) REVERT: I 488 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6232 (pm20) REVERT: J 138 GLN cc_start: 0.7768 (mp10) cc_final: 0.7422 (mp10) REVERT: J 211 LYS cc_start: 0.6144 (mttt) cc_final: 0.5874 (mmmt) REVERT: J 256 ILE cc_start: 0.4688 (mp) cc_final: 0.3088 (mt) REVERT: M 106 PHE cc_start: 0.2434 (OUTLIER) cc_final: 0.1555 (m-80) REVERT: M 262 TYR cc_start: 0.5511 (t80) cc_final: 0.5193 (t80) REVERT: M 474 ASP cc_start: 0.5217 (t0) cc_final: 0.4556 (t0) REVERT: M 481 ARG cc_start: 0.6639 (tpp80) cc_final: 0.6335 (ttt180) REVERT: N 2 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7658 (ptp-170) REVERT: N 44 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5818 (m-30) REVERT: N 158 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.5087 (t80) REVERT: N 192 TRP cc_start: 0.6326 (p-90) cc_final: 0.5921 (p-90) REVERT: N 414 MET cc_start: 0.6875 (mmm) cc_final: 0.6529 (mmm) outliers start: 173 outliers final: 108 residues processed: 722 average time/residue: 0.4801 time to fit residues: 553.0536 Evaluate side-chains 705 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 589 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 ASP 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 378 LEU Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 111 HIS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 303 ASP 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 J residue 430 LEU Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 VAL 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 462 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 158 PHE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 214 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain N residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 1.9990 chunk 208 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 253 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN B 286 GLN E 47 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 163 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 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 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 360 HIS M 454 GLN N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 35032 Z= 0.375 Angle : 0.747 12.098 48160 Z= 0.397 Chirality : 0.048 0.250 5276 Planarity : 0.006 0.062 5488 Dihedral : 18.777 85.999 6388 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.83 % Allowed : 30.95 % Favored : 62.23 % 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: -1.68 (0.13), residues: 3636 helix: -0.08 (0.14), residues: 1274 sheet: -1.29 (0.21), residues: 570 loop : -1.81 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 294 HIS 0.058 0.003 HIS A 251 PHE 0.030 0.002 PHE F 45 TYR 0.027 0.002 TYR A 411 ARG 0.015 0.001 ARG M 72 *********************** 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 863 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 639 time to evaluate : 3.474 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 251 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5635 (m-70) REVERT: A 406 MET cc_start: 0.7027 (tmm) cc_final: 0.6823 (tmm) REVERT: E 137 ASP cc_start: 0.7138 (m-30) cc_final: 0.6684 (m-30) REVERT: E 227 SER cc_start: 0.6078 (p) cc_final: 0.5772 (p) REVERT: E 296 ASN cc_start: 0.6426 (m-40) cc_final: 0.6108 (m-40) REVERT: E 462 LEU cc_start: 0.7589 (mm) cc_final: 0.7376 (mp) REVERT: F 135 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5612 (t80) REVERT: F 157 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.4732 (tt) REVERT: F 161 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.5793 (m-30) REVERT: F 324 SER cc_start: 0.7487 (t) cc_final: 0.7210 (p) REVERT: F 414 MET cc_start: 0.6862 (ppp) cc_final: 0.6614 (ppp) REVERT: I 35 GLN cc_start: 0.7036 (tp40) cc_final: 0.6787 (tp40) REVERT: I 488 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: J 86 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8592 (mtpt) REVERT: J 256 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4030 (mt) REVERT: J 430 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.4935 (mp) REVERT: J 433 ILE cc_start: 0.7373 (pt) cc_final: 0.7082 (mt) REVERT: M 106 PHE cc_start: 0.2649 (OUTLIER) cc_final: 0.1954 (m-80) REVERT: M 148 TYR cc_start: 0.6705 (t80) cc_final: 0.6392 (t80) REVERT: M 435 MET cc_start: 0.8003 (tmm) cc_final: 0.7553 (tmm) REVERT: N 181 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.5363 (p90) REVERT: N 192 TRP cc_start: 0.6601 (p-90) cc_final: 0.6329 (p-90) REVERT: N 414 MET cc_start: 0.7412 (mmm) cc_final: 0.7060 (mmm) outliers start: 224 outliers final: 153 residues processed: 766 average time/residue: 0.4868 time to fit residues: 596.5576 Evaluate side-chains 757 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 595 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 384 VAL 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 470 CYS 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 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 THR 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 368 TRP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 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 384 LEU Chi-restraints excluded: chain F residue 389 ASN 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 60 ILE Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 426 VAL Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 34 CYS Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 199 ASP 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 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 441 ILE Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 191 ASP Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 224 ILE 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 341 ILE Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 426 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 0.6980 chunk 330 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 367 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 251 HIS A 295 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS I 201 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** J 357 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 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN M 360 HIS N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35032 Z= 0.318 Angle : 0.712 14.207 48160 Z= 0.373 Chirality : 0.047 0.336 5276 Planarity : 0.005 0.063 5488 Dihedral : 18.833 89.335 6388 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 6.80 % Allowed : 31.77 % Favored : 61.43 % 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: -1.71 (0.13), residues: 3636 helix: -0.09 (0.14), residues: 1272 sheet: -1.40 (0.21), residues: 550 loop : -1.81 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 294 HIS 0.013 0.001 HIS I 111 PHE 0.030 0.002 PHE F 411 TYR 0.036 0.002 TYR M 285 ARG 0.020 0.001 ARG B 374 *********************** 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 838 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 615 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 HIS cc_start: 0.5535 (OUTLIER) cc_final: 0.5089 (m90) REVERT: A 303 MET cc_start: 0.7535 (tmm) cc_final: 0.7287 (tmm) REVERT: A 406 MET cc_start: 0.7003 (tmm) cc_final: 0.6652 (tmm) REVERT: A 435 MET cc_start: 0.7828 (tpp) cc_final: 0.7558 (tpp) REVERT: B 105 TYR cc_start: 0.7392 (t80) cc_final: 0.7156 (t80) REVERT: E 227 SER cc_start: 0.5925 (p) cc_final: 0.5609 (p) REVERT: E 294 PRO cc_start: 0.6580 (Cg_exo) cc_final: 0.6338 (Cg_endo) REVERT: E 296 ASN cc_start: 0.6324 (m-40) cc_final: 0.6073 (m-40) REVERT: E 503 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.4549 (t80) REVERT: F 135 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.5488 (t80) REVERT: F 157 ILE cc_start: 0.5550 (OUTLIER) cc_final: 0.5073 (tt) REVERT: F 324 SER cc_start: 0.7654 (t) cc_final: 0.7394 (p) REVERT: F 336 MET cc_start: 0.6269 (mpp) cc_final: 0.5581 (mpp) REVERT: I 349 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5926 (mt0) REVERT: I 488 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: J 159 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7997 (tt) REVERT: J 211 LYS cc_start: 0.4695 (mttp) cc_final: 0.3529 (mmmt) REVERT: J 256 ILE cc_start: 0.5346 (OUTLIER) cc_final: 0.3398 (mt) REVERT: J 430 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4851 (mp) REVERT: J 433 ILE cc_start: 0.7291 (pt) cc_final: 0.6968 (mt) REVERT: M 52 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7487 (mm) REVERT: M 106 PHE cc_start: 0.2622 (OUTLIER) cc_final: 0.1940 (m-80) REVERT: M 435 MET cc_start: 0.7716 (tmm) cc_final: 0.6996 (tmm) REVERT: N 92 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7173 (tpp) REVERT: N 181 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5437 (p90) REVERT: N 192 TRP cc_start: 0.6701 (p-90) cc_final: 0.6497 (p-90) REVERT: N 414 MET cc_start: 0.7370 (mmm) cc_final: 0.7139 (mmm) outliers start: 223 outliers final: 161 residues processed: 749 average time/residue: 0.4547 time to fit residues: 540.6367 Evaluate side-chains 772 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 598 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 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 367 ASP 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 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 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 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 183 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 290 THR Chi-restraints excluded: chain B residue 328 LYS 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 391 ILE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 503 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 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 153 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 229 LYS 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 274 GLU 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 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 86 TRP 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 349 GLN Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 232 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 268 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 430 LEU Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 409 ASN Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 69 ASN 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 108 ILE Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 258 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 426 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 chunk 309 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 366 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 chunk 223 optimal weight: 0.4980 chunk 169 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS E 47 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS ** F 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN I 111 HIS I 201 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN 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 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.4232 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= 0.215 Angle : 0.664 15.306 48160 Z= 0.348 Chirality : 0.044 0.273 5276 Planarity : 0.005 0.063 5488 Dihedral : 18.781 89.362 6388 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 5.73 % Allowed : 33.14 % Favored : 61.13 % 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: -1.60 (0.13), residues: 3636 helix: 0.08 (0.14), residues: 1262 sheet: -1.41 (0.22), residues: 528 loop : -1.79 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 294 HIS 0.021 0.001 HIS A 251 PHE 0.030 0.001 PHE A 442 TYR 0.034 0.001 TYR M 285 ARG 0.012 0.001 ARG A 113 *********************** 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 815 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 627 time to evaluate : 3.161 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: B 105 TYR cc_start: 0.7355 (t80) cc_final: 0.7075 (t80) REVERT: B 171 TYR cc_start: 0.6843 (m-80) cc_final: 0.6637 (m-80) REVERT: B 219 TRP cc_start: 0.5709 (m100) cc_final: 0.5410 (m100) REVERT: E 24 ARG cc_start: 0.6336 (mpp80) cc_final: 0.6021 (mtm180) REVERT: E 137 ASP cc_start: 0.6807 (m-30) cc_final: 0.6353 (m-30) REVERT: E 227 SER cc_start: 0.5837 (p) cc_final: 0.5521 (p) REVERT: E 364 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5979 (mtm-85) REVERT: F 135 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5445 (t80) REVERT: F 324 SER cc_start: 0.7685 (t) cc_final: 0.7443 (p) REVERT: F 336 MET cc_start: 0.6147 (mpp) cc_final: 0.5545 (mpp) REVERT: I 349 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5894 (mt0) REVERT: I 488 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: J 256 ILE cc_start: 0.5042 (OUTLIER) cc_final: 0.3087 (tp) REVERT: J 430 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4799 (mp) REVERT: M 52 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7440 (mm) REVERT: M 106 PHE cc_start: 0.2533 (OUTLIER) cc_final: 0.1954 (m-80) REVERT: M 435 MET cc_start: 0.7456 (tmm) cc_final: 0.6774 (tmm) REVERT: N 14 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: N 92 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7274 (tpp) REVERT: N 287 MET cc_start: 0.4200 (tpt) cc_final: 0.3736 (tpt) REVERT: N 414 MET cc_start: 0.7286 (mmm) cc_final: 0.7042 (mmm) outliers start: 188 outliers final: 140 residues processed: 734 average time/residue: 0.4660 time to fit residues: 540.6183 Evaluate side-chains 744 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 594 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 ASP 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 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 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 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 328 LYS 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 391 ILE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 445 ILE 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 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 208 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 274 GLU 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 401 ILE Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 200 TYR Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 357 GLN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 378 LEU 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 430 LEU 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 55 SER Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 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 44 ASP 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 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 258 ASN Chi-restraints excluded: chain N residue 293 TYR Chi-restraints excluded: chain N residue 341 ILE Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 426 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.0020 chunk 146 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 70 optimal weight: 0.7980 chunk 232 optimal weight: 0.3980 chunk 249 optimal weight: 0.8980 chunk 181 optimal weight: 0.0570 chunk 34 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 overall best weight: 0.2704 ------------------------------------------------------------------------------- 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 251 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN E 47 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS I 201 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** J 364 GLN ** 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 446 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35032 Z= 0.192 Angle : 0.673 16.497 48160 Z= 0.349 Chirality : 0.044 0.387 5276 Planarity : 0.005 0.069 5488 Dihedral : 18.703 88.384 6388 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.85 % Allowed : 34.24 % Favored : 60.91 % 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: -1.51 (0.13), residues: 3636 helix: 0.15 (0.14), residues: 1260 sheet: -1.25 (0.22), residues: 548 loop : -1.76 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 294 HIS 0.008 0.001 HIS I 207 PHE 0.031 0.001 PHE A 442 TYR 0.029 0.001 TYR E 6 ARG 0.010 0.000 ARG A 113 *********************** 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 779 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 620 time to evaluate : 3.556 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: A 1 MET cc_start: 0.1260 (tpp) cc_final: 0.0399 (tpt) REVERT: A 251 HIS cc_start: 0.4899 (OUTLIER) cc_final: 0.4535 (m90) REVERT: A 303 MET cc_start: 0.7763 (tmm) cc_final: 0.7448 (tmm) REVERT: B 105 TYR cc_start: 0.7292 (t80) cc_final: 0.7014 (t80) REVERT: B 193 ARG cc_start: 0.5087 (ptt-90) cc_final: 0.4853 (ptp90) REVERT: B 308 ILE cc_start: 0.5141 (tt) cc_final: 0.4867 (tt) REVERT: E 227 SER cc_start: 0.6028 (p) cc_final: 0.5691 (p) REVERT: E 364 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.5928 (mtm-85) REVERT: F 135 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5221 (t80) REVERT: F 324 SER cc_start: 0.7699 (t) cc_final: 0.7484 (p) REVERT: F 336 MET cc_start: 0.6092 (mpp) cc_final: 0.5547 (mpp) REVERT: I 349 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5809 (mt0) REVERT: I 420 LEU cc_start: 0.6380 (tp) cc_final: 0.6153 (tp) REVERT: I 488 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: J 92 MET cc_start: 0.7597 (mtp) cc_final: 0.7328 (mtp) REVERT: J 114 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7431 (tpp-160) REVERT: J 256 ILE cc_start: 0.5148 (OUTLIER) cc_final: 0.3104 (tp) REVERT: J 399 GLU cc_start: 0.3682 (tp30) cc_final: 0.3142 (tp30) REVERT: M 52 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7429 (mm) REVERT: M 106 PHE cc_start: 0.2383 (OUTLIER) cc_final: 0.1717 (m-80) REVERT: M 435 MET cc_start: 0.7490 (tmm) cc_final: 0.6928 (tmm) REVERT: N 2 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7757 (ptp-170) REVERT: N 92 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7392 (tpp) REVERT: N 181 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5261 (p90) REVERT: N 414 MET cc_start: 0.7144 (mmm) cc_final: 0.6878 (mmm) REVERT: N 426 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6157 (tp30) outliers start: 159 outliers final: 122 residues processed: 710 average time/residue: 0.4720 time to fit residues: 531.5688 Evaluate side-chains 727 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 593 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU 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 127 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU 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 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 340 THR 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 F residue 1 MET Chi-restraints excluded: chain F residue 62 ILE 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 221 TYR Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 201 ASN Chi-restraints excluded: chain I residue 287 LYS Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 265 ILE Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 357 GLN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 401 ILE Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 247 LYS Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 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 216 THR Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 234 ASN 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 332 SER Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 426 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 0.7980 chunk 350 optimal weight: 3.9990 chunk 320 optimal weight: 0.6980 chunk 341 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 308 optimal weight: 0.3980 chunk 322 optimal weight: 1.9990 chunk 340 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 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 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN I 201 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 GLN ** J 364 GLN ** 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 446 ASN N 69 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35032 Z= 0.227 Angle : 0.697 15.937 48160 Z= 0.362 Chirality : 0.045 0.428 5276 Planarity : 0.005 0.150 5488 Dihedral : 18.718 87.721 6388 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 4.91 % Allowed : 34.21 % Favored : 60.88 % 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: -1.53 (0.13), residues: 3636 helix: 0.15 (0.14), residues: 1236 sheet: -1.30 (0.22), residues: 528 loop : -1.75 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP J 369 HIS 0.007 0.001 HIS I 207 PHE 0.047 0.001 PHE A 30 TYR 0.022 0.001 TYR I 202 ARG 0.020 0.001 ARG E 113 *********************** 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 767 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 606 time to evaluate : 3.533 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: A 303 MET cc_start: 0.7907 (tmm) cc_final: 0.7600 (tmm) REVERT: B 105 TYR cc_start: 0.7368 (t80) cc_final: 0.7085 (t80) REVERT: B 378 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7100 (mp) REVERT: E 137 ASP cc_start: 0.6639 (m-30) cc_final: 0.6284 (m-30) REVERT: E 227 SER cc_start: 0.6298 (p) cc_final: 0.5951 (p) REVERT: E 364 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.5922 (mtm-85) REVERT: F 135 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.5380 (t80) REVERT: F 263 ARG cc_start: 0.4288 (OUTLIER) cc_final: 0.3990 (ttt90) REVERT: F 324 SER cc_start: 0.7751 (t) cc_final: 0.7518 (p) REVERT: F 336 MET cc_start: 0.6067 (mpp) cc_final: 0.5540 (mpp) REVERT: I 86 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.6922 (t-100) REVERT: I 209 GLN cc_start: 0.6283 (tp-100) cc_final: 0.5841 (tt0) REVERT: I 349 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6260 (mt0) REVERT: I 488 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6263 (pm20) REVERT: J 92 MET cc_start: 0.7635 (mtp) cc_final: 0.7284 (mtp) REVERT: J 114 ARG cc_start: 0.8021 (mmp80) cc_final: 0.7439 (tpp-160) REVERT: J 256 ILE cc_start: 0.5209 (OUTLIER) cc_final: 0.3241 (tp) REVERT: J 399 GLU cc_start: 0.3845 (tp30) cc_final: 0.3290 (tp30) REVERT: M 52 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7468 (mm) REVERT: M 435 MET cc_start: 0.7507 (tmm) cc_final: 0.6914 (tmm) REVERT: N 92 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: N 181 PHE cc_start: 0.6262 (OUTLIER) cc_final: 0.5369 (p90) REVERT: N 287 MET cc_start: 0.4110 (tpt) cc_final: 0.3566 (tpt) REVERT: N 414 MET cc_start: 0.7128 (mmm) cc_final: 0.6838 (mmm) outliers start: 161 outliers final: 131 residues processed: 704 average time/residue: 0.4926 time to fit residues: 553.3998 Evaluate side-chains 736 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 594 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 127 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 462 LEU 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 44 ASP 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 262 GLN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 THR 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 378 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 340 THR 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 493 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 229 LYS Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 263 ARG Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 PHE Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 287 LYS Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 222 ASP 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 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 401 ILE Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 234 ASN 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 332 SER Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.0970 chunk 360 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 250 optimal weight: 0.8980 chunk 378 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** E 61 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** ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** 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 446 ASN N 349 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35032 Z= 0.230 Angle : 0.718 15.903 48160 Z= 0.371 Chirality : 0.045 0.447 5276 Planarity : 0.005 0.144 5488 Dihedral : 18.742 88.638 6388 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 4.76 % Allowed : 34.63 % Favored : 60.61 % 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: -1.56 (0.13), residues: 3636 helix: 0.08 (0.14), residues: 1250 sheet: -1.27 (0.22), residues: 528 loop : -1.76 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP J 369 HIS 0.007 0.001 HIS I 207 PHE 0.054 0.002 PHE A 30 TYR 0.019 0.001 TYR F 293 ARG 0.015 0.001 ARG E 113 ********************** 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 763 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 607 time to evaluate : 3.785 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: A 251 HIS cc_start: 0.4886 (OUTLIER) cc_final: 0.4471 (m90) REVERT: A 303 MET cc_start: 0.7888 (tmm) cc_final: 0.7588 (tmm) REVERT: B 105 TYR cc_start: 0.7346 (t80) cc_final: 0.7062 (t80) REVERT: B 308 ILE cc_start: 0.5281 (tt) cc_final: 0.5054 (tt) REVERT: B 378 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7057 (mp) REVERT: E 137 ASP cc_start: 0.6641 (m-30) cc_final: 0.6289 (m-30) REVERT: E 227 SER cc_start: 0.6238 (p) cc_final: 0.5948 (p) REVERT: E 364 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.5939 (mtm-85) REVERT: F 135 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5378 (t80) REVERT: F 157 ILE cc_start: 0.5658 (tp) cc_final: 0.5283 (tp) REVERT: F 324 SER cc_start: 0.7742 (t) cc_final: 0.7478 (p) REVERT: F 336 MET cc_start: 0.6058 (mpp) cc_final: 0.5572 (mpp) REVERT: I 209 GLN cc_start: 0.6189 (tp-100) cc_final: 0.5789 (tt0) REVERT: I 349 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5938 (mt0) REVERT: I 488 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6280 (pm20) REVERT: J 92 MET cc_start: 0.7691 (mtp) cc_final: 0.7302 (mtp) REVERT: J 399 GLU cc_start: 0.3709 (tp30) cc_final: 0.3184 (tp30) REVERT: M 52 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7480 (mm) REVERT: M 106 PHE cc_start: 0.2536 (OUTLIER) cc_final: 0.1946 (m-80) REVERT: M 435 MET cc_start: 0.7543 (tmm) cc_final: 0.6941 (tmm) REVERT: N 28 LEU cc_start: 0.7389 (tp) cc_final: 0.7135 (tp) REVERT: N 92 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7372 (tpp) REVERT: N 181 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5176 (p90) REVERT: N 414 MET cc_start: 0.7130 (mmm) cc_final: 0.6852 (mmm) outliers start: 156 outliers final: 129 residues processed: 699 average time/residue: 0.4739 time to fit residues: 528.1321 Evaluate side-chains 731 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 592 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 127 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 367 ASP 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 460 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 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 44 ASP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 183 ASN 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 290 THR Chi-restraints excluded: chain B residue 328 LYS 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 378 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 389 ASN 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 41 SER Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 488 GLU Chi-restraints excluded: chain I residue 505 TYR Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 222 ASP 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 290 THR Chi-restraints excluded: chain J residue 291 PHE Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 349 ASN Chi-restraints excluded: chain J residue 371 ASP Chi-restraints excluded: chain J residue 372 LYS Chi-restraints excluded: chain J residue 392 TYR Chi-restraints excluded: chain J residue 401 ILE Chi-restraints excluded: chain J residue 414 MET Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 106 PHE Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 233 ASP Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 423 LEU Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 443 ILE Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 181 PHE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 215 CYS Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 232 THR Chi-restraints excluded: chain N residue 234 ASN 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 332 SER Chi-restraints excluded: chain N residue 349 ASN Chi-restraints excluded: chain N residue 370 ASN Chi-restraints excluded: chain N residue 395 VAL Chi-restraints excluded: chain N residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 92 optimal weight: 0.0070 chunk 277 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 55 optimal weight: 0.0670 overall best weight: 0.6336 ------------------------------------------------------------------------------- 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 251 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** E 61 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** ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 314 GLN ** 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 446 ASN ** N 69 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 = 0.4615 r_free = 0.4615 target = 0.180392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.148264 restraints weight = 69998.080| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 4.34 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 35032 Z= 0.308 Angle : 0.829 59.200 48160 Z= 0.447 Chirality : 0.047 0.749 5276 Planarity : 0.006 0.140 5488 Dihedral : 18.757 88.685 6388 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 4.82 % Allowed : 34.42 % Favored : 60.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1250 sheet: -1.27 (0.22), residues: 528 loop : -1.77 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP E 370 HIS 0.085 0.002 HIS A 251 PHE 0.064 0.002 PHE A 30 TYR 0.020 0.001 TYR F 293 ARG 0.034 0.001 ARG J 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9555.17 seconds wall clock time: 172 minutes 36.88 seconds (10356.88 seconds total)