Starting phenix.real_space_refine on Sun May 3 13:09:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v3e_64753/05_2026/9v3e_64753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v3e_64753/05_2026/9v3e_64753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v3e_64753/05_2026/9v3e_64753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v3e_64753/05_2026/9v3e_64753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v3e_64753/05_2026/9v3e_64753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v3e_64753/05_2026/9v3e_64753.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8298 2.51 5 N 2175 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13119 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3417 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 16, 'TRANS': 428} Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 900 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "B" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3417 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 16, 'TRANS': 428} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 900 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "C" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3417 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 16, 'TRANS': 428} Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 900 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.60, per 1000 atoms: 0.27 Number of scatterers: 13119 At special positions: 0 Unit cell: (133, 130.15, 104.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2565 8.00 N 2175 7.00 C 8298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.02 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 105 " distance=2.02 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 105 " distance=2.02 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.02 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 105 " distance=2.02 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG A 602 " - " ASN A 99 " " NAG A 603 " - " ASN A 414 " " NAG A 604 " - " ASN A 464 " " NAG B 601 " - " ASN B 67 " " NAG B 602 " - " ASN B 99 " " NAG B 603 " - " ASN B 414 " " NAG B 604 " - " ASN B 464 " " NAG C 601 " - " ASN C 67 " " NAG C 602 " - " ASN C 99 " " NAG C 603 " - " ASN C 414 " " NAG C 604 " - " ASN C 464 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 660.3 milliseconds 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3162 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 33.0% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 74 through 100 Proline residue: A 89 - end of helix removed outlier: 4.031A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 146 removed outlier: 4.215A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.533A pdb=" N LEU A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.090A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.640A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 470 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.563A pdb=" N LEU E 15 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 79 Processing helix chain 'B' and resid 29 through 36 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 74 through 100 Proline residue: B 89 - end of helix removed outlier: 4.032A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.215A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.534A pdb=" N LEU B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.091A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.640A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 470 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.563A pdb=" N LEU F 15 " --> pdb=" O PRO F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 74 through 100 Proline residue: C 89 - end of helix removed outlier: 4.031A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 4.215A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.533A pdb=" N LEU C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 4.090A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.640A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 470 Processing helix chain 'G' and resid 10 through 15 removed outlier: 3.563A pdb=" N LEU G 15 " --> pdb=" O PRO G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 17.026A pdb=" N THR A 168 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N THR A 54 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N TYR A 170 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP A 56 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N PHE A 172 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 58 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.980A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.687A pdb=" N VAL A 113 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N SER C 428 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET A 115 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 removed outlier: 6.098A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 46 through 48 removed outlier: 4.274A pdb=" N TRP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 162 removed outlier: 17.025A pdb=" N THR B 168 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N THR B 54 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 11.107A pdb=" N TYR B 170 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP B 56 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N PHE B 172 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 58 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 38 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 296 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS B 40 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN B 294 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N VAL B 42 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N TYR B 292 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ARG B 44 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N GLN B 290 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR B 46 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB2, first strand: chain 'B' and resid 226 through 227 removed outlier: 3.980A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR B 46 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N GLN B 290 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ARG B 44 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N TYR B 292 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N VAL B 42 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN B 294 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS B 40 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 296 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 38 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 303 removed outlier: 6.098A pdb=" N ARG B 365 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 46 through 48 removed outlier: 4.275A pdb=" N TRP F 41 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 162 removed outlier: 17.026A pdb=" N THR C 168 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N THR C 54 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N TYR C 170 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP C 56 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N PHE C 172 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 58 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 38 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 296 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS C 40 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN C 294 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N VAL C 42 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N TYR C 292 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ARG C 44 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N GLN C 290 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR C 46 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE C 282 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR C 54 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 280 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP C 56 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 278 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL C 58 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 276 " --> pdb=" O VAL C 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 275 through 298 current: chain 'C' and resid 332 through 333 Processing sheet with id=AB9, first strand: chain 'C' and resid 226 through 227 removed outlier: 3.979A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 276 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL C 58 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 278 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP C 56 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 280 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR C 54 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE C 282 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR C 46 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N GLN C 290 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ARG C 44 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N TYR C 292 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N VAL C 42 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N GLN C 294 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS C 40 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 296 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 38 " --> pdb=" O LEU C 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 322 through 326 Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.097A pdb=" N ARG C 365 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'G' and resid 46 through 48 removed outlier: 4.275A pdb=" N TRP G 41 " --> pdb=" O VAL G 48 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4230 1.34 - 1.45: 1850 1.45 - 1.57: 7153 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 13347 Sorted by residual: bond pdb=" C LEU A 38 " pdb=" N VAL A 39 " ideal model delta sigma weight residual 1.333 1.315 0.018 1.20e-02 6.94e+03 2.22e+00 bond pdb=" C LEU B 38 " pdb=" N VAL B 39 " ideal model delta sigma weight residual 1.333 1.315 0.018 1.20e-02 6.94e+03 2.15e+00 bond pdb=" C LEU C 38 " pdb=" N VAL C 39 " ideal model delta sigma weight residual 1.333 1.315 0.017 1.20e-02 6.94e+03 2.12e+00 bond pdb=" CA VAL C 312 " pdb=" CB VAL C 312 " ideal model delta sigma weight residual 1.547 1.533 0.014 1.10e-02 8.26e+03 1.69e+00 bond pdb=" CB GLU A 406 " pdb=" CG GLU A 406 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 ... (remaining 13342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 17271 1.44 - 2.88: 740 2.88 - 4.32: 103 4.32 - 5.76: 33 5.76 - 7.20: 6 Bond angle restraints: 18153 Sorted by residual: angle pdb=" CA GLU B 406 " pdb=" CB GLU B 406 " pdb=" CG GLU B 406 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA GLU C 406 " pdb=" CB GLU C 406 " pdb=" CG GLU C 406 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" CA GLU A 406 " pdb=" CB GLU A 406 " pdb=" CG GLU A 406 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C ARG E 40 " pdb=" CA ARG E 40 " pdb=" CB ARG E 40 " ideal model delta sigma weight residual 110.14 115.36 -5.22 1.54e+00 4.22e-01 1.15e+01 angle pdb=" C ARG F 40 " pdb=" CA ARG F 40 " pdb=" CB ARG F 40 " ideal model delta sigma weight residual 110.14 115.32 -5.18 1.54e+00 4.22e-01 1.13e+01 ... (remaining 18148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 7571 17.18 - 34.36: 529 34.36 - 51.55: 147 51.55 - 68.73: 60 68.73 - 85.91: 18 Dihedral angle restraints: 8325 sinusoidal: 3432 harmonic: 4893 Sorted by residual: dihedral pdb=" CB CYS F 6 " pdb=" SG CYS F 6 " pdb=" SG CYS F 105 " pdb=" CB CYS F 105 " ideal model delta sinusoidal sigma weight residual -86.00 -167.12 81.12 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 105 " pdb=" CB CYS G 105 " ideal model delta sinusoidal sigma weight residual -86.00 -167.10 81.10 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS E 6 " pdb=" SG CYS E 6 " pdb=" SG CYS E 105 " pdb=" CB CYS E 105 " ideal model delta sinusoidal sigma weight residual -86.00 -167.07 81.07 1 1.00e+01 1.00e-02 8.11e+01 ... (remaining 8322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1491 0.046 - 0.092: 530 0.092 - 0.138: 176 0.138 - 0.183: 8 0.183 - 0.229: 3 Chirality restraints: 2208 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2205 not shown) Planarity restraints: 2298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 54 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO F 55 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 55 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 55 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 54 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO G 55 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 54 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 55 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.024 5.00e-02 4.00e+02 ... (remaining 2295 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2787 2.78 - 3.31: 12264 3.31 - 3.84: 22140 3.84 - 4.37: 26776 4.37 - 4.90: 46109 Nonbonded interactions: 110076 Sorted by model distance: nonbonded pdb=" O MET C 61 " pdb=" OH TYR C 79 " model vdw 2.245 3.040 nonbonded pdb=" O MET B 61 " pdb=" OH TYR B 79 " model vdw 2.246 3.040 nonbonded pdb=" O MET A 61 " pdb=" OH TYR A 79 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR B 334 " pdb=" O SER B 337 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" O SER A 337 " model vdw 2.256 3.040 ... (remaining 110071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 9.010 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.007 0.039 13377 Z= 0.294 Angle : 0.701 7.196 18225 Z= 0.379 Chirality : 0.050 0.229 2208 Planarity : 0.004 0.044 2286 Dihedral : 14.309 85.912 5109 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1659 helix: 1.09 (0.25), residues: 450 sheet: -0.20 (0.24), residues: 420 loop : -1.68 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 244 TYR 0.012 0.001 TYR B 135 PHE 0.012 0.002 PHE C 253 TRP 0.009 0.001 TRP F 52 HIS 0.002 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00678 (13347) covalent geometry : angle 0.69410 (18153) SS BOND : bond 0.00669 ( 18) SS BOND : angle 1.74795 ( 36) hydrogen bonds : bond 0.14290 ( 537) hydrogen bonds : angle 6.65754 ( 1503) link_NAG-ASN : bond 0.00250 ( 12) link_NAG-ASN : angle 1.65671 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7428 (tttp) cc_final: 0.7116 (ttmt) REVERT: C 411 MET cc_start: 0.8100 (tmm) cc_final: 0.7880 (tmm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1349 time to fit residues: 42.5722 Evaluate side-chains 114 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079231 restraints weight = 22796.443| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.22 r_work: 0.2943 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13377 Z= 0.155 Angle : 0.540 8.219 18225 Z= 0.284 Chirality : 0.046 0.174 2208 Planarity : 0.004 0.044 2286 Dihedral : 5.651 52.038 2034 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.07 % Allowed : 6.69 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1659 helix: 1.16 (0.24), residues: 474 sheet: 0.16 (0.25), residues: 396 loop : -1.41 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 353 TYR 0.011 0.001 TYR B 248 PHE 0.013 0.001 PHE B 253 TRP 0.004 0.001 TRP B 308 HIS 0.006 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00362 (13347) covalent geometry : angle 0.53446 (18153) SS BOND : bond 0.00319 ( 18) SS BOND : angle 1.45873 ( 36) hydrogen bonds : bond 0.03861 ( 537) hydrogen bonds : angle 5.14998 ( 1503) link_NAG-ASN : bond 0.00203 ( 12) link_NAG-ASN : angle 1.26244 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7284 (tttp) cc_final: 0.6832 (ttmt) REVERT: A 196 GLU cc_start: 0.8495 (tt0) cc_final: 0.8211 (tt0) REVERT: A 336 ARG cc_start: 0.8368 (ptm160) cc_final: 0.8088 (tpt-90) REVERT: E 104 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8348 (mp0) REVERT: F 107 ILE cc_start: 0.8099 (tt) cc_final: 0.7651 (tp) REVERT: C 36 ILE cc_start: 0.8756 (tt) cc_final: 0.8534 (tt) REVERT: C 411 MET cc_start: 0.8890 (tmm) cc_final: 0.8475 (tmm) outliers start: 16 outliers final: 11 residues processed: 170 average time/residue: 0.1263 time to fit residues: 30.6034 Evaluate side-chains 131 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 131 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 139 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078250 restraints weight = 23059.031| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.23 r_work: 0.2927 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13377 Z= 0.156 Angle : 0.525 7.411 18225 Z= 0.275 Chirality : 0.046 0.177 2208 Planarity : 0.004 0.038 2286 Dihedral : 5.082 46.391 2034 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.94 % Allowed : 10.84 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1659 helix: 1.47 (0.24), residues: 468 sheet: 0.14 (0.25), residues: 396 loop : -1.28 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 65 TYR 0.012 0.001 TYR A 248 PHE 0.012 0.001 PHE A 282 TRP 0.005 0.001 TRP G 77 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00365 (13347) covalent geometry : angle 0.52023 (18153) SS BOND : bond 0.00326 ( 18) SS BOND : angle 1.25372 ( 36) hydrogen bonds : bond 0.03683 ( 537) hydrogen bonds : angle 4.91393 ( 1503) link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 1.30766 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7350 (tttp) cc_final: 0.6938 (ttpt) REVERT: A 196 GLU cc_start: 0.8454 (tt0) cc_final: 0.8113 (tt0) REVERT: A 226 MET cc_start: 0.8371 (ttm) cc_final: 0.8166 (ttp) REVERT: A 336 ARG cc_start: 0.8382 (ptm160) cc_final: 0.8125 (tpt-90) REVERT: E 65 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8410 (mtp-110) REVERT: E 104 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8383 (mp0) REVERT: F 107 ILE cc_start: 0.8050 (tt) cc_final: 0.7765 (tp) REVERT: C 36 ILE cc_start: 0.8754 (tt) cc_final: 0.8520 (tt) REVERT: C 353 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7750 (ttp80) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.1357 time to fit residues: 26.8067 Evaluate side-chains 133 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 GLN F 100 GLN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.076057 restraints weight = 23044.692| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.20 r_work: 0.2884 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13377 Z= 0.229 Angle : 0.565 6.747 18225 Z= 0.292 Chirality : 0.048 0.189 2208 Planarity : 0.004 0.032 2286 Dihedral : 5.146 49.508 2034 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.67 % Allowed : 10.91 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1659 helix: 1.39 (0.24), residues: 474 sheet: 0.05 (0.25), residues: 411 loop : -1.36 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 399 TYR 0.018 0.001 TYR A 248 PHE 0.015 0.002 PHE A 282 TRP 0.005 0.001 TRP B 308 HIS 0.004 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00548 (13347) covalent geometry : angle 0.55828 (18153) SS BOND : bond 0.00565 ( 18) SS BOND : angle 1.48322 ( 36) hydrogen bonds : bond 0.03837 ( 537) hydrogen bonds : angle 4.93936 ( 1503) link_NAG-ASN : bond 0.00218 ( 12) link_NAG-ASN : angle 1.41870 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8620 (tt0) cc_final: 0.8353 (tt0) REVERT: A 336 ARG cc_start: 0.8465 (ptm160) cc_final: 0.8238 (tpt-90) REVERT: E 104 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8402 (mp0) REVERT: C 36 ILE cc_start: 0.8850 (tt) cc_final: 0.8572 (tt) REVERT: C 353 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7774 (ttp80) REVERT: C 411 MET cc_start: 0.8951 (tmm) cc_final: 0.8724 (tmm) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.1194 time to fit residues: 25.6602 Evaluate side-chains 138 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain G residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 18 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 58 optimal weight: 0.2980 chunk 126 optimal weight: 0.0980 chunk 160 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 HIS C 395 GLN G 32 HIS ** G 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080298 restraints weight = 22674.610| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.19 r_work: 0.2962 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13377 Z= 0.106 Angle : 0.480 7.115 18225 Z= 0.252 Chirality : 0.045 0.176 2208 Planarity : 0.003 0.029 2286 Dihedral : 4.572 47.089 2034 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.54 % Allowed : 12.25 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1659 helix: 1.67 (0.24), residues: 468 sheet: 0.17 (0.26), residues: 381 loop : -1.11 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.010 0.001 TYR A 248 PHE 0.009 0.001 PHE B 282 TRP 0.006 0.001 TRP F 98 HIS 0.003 0.000 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00237 (13347) covalent geometry : angle 0.47530 (18153) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.14546 ( 36) hydrogen bonds : bond 0.03205 ( 537) hydrogen bonds : angle 4.71582 ( 1503) link_NAG-ASN : bond 0.00173 ( 12) link_NAG-ASN : angle 1.23446 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.450 Fit side-chains REVERT: A 196 GLU cc_start: 0.8458 (tt0) cc_final: 0.8171 (tm-30) REVERT: A 336 ARG cc_start: 0.8379 (ptm160) cc_final: 0.8140 (tpt-90) REVERT: A 355 CYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9135 (t) REVERT: E 40 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8396 (mtm-85) REVERT: E 65 ARG cc_start: 0.8584 (mtp-110) cc_final: 0.8380 (mtp-110) REVERT: E 104 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8346 (mp0) REVERT: B 220 ASP cc_start: 0.8430 (m-30) cc_final: 0.7870 (p0) REVERT: F 40 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.8207 (mtp85) REVERT: C 36 ILE cc_start: 0.8726 (tt) cc_final: 0.8493 (tt) REVERT: G 79 ASN cc_start: 0.8483 (m-40) cc_final: 0.7171 (t0) REVERT: G 98 TRP cc_start: 0.8444 (t60) cc_final: 0.8215 (t60) outliers start: 23 outliers final: 11 residues processed: 159 average time/residue: 0.1260 time to fit residues: 28.7156 Evaluate side-chains 139 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 81 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN F 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078313 restraints weight = 22873.338| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.21 r_work: 0.2919 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13377 Z= 0.157 Angle : 0.511 6.986 18225 Z= 0.265 Chirality : 0.046 0.168 2208 Planarity : 0.003 0.053 2286 Dihedral : 4.503 38.198 2034 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.67 % Allowed : 12.78 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1659 helix: 1.66 (0.24), residues: 468 sheet: 0.17 (0.27), residues: 381 loop : -1.10 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 353 TYR 0.013 0.001 TYR A 248 PHE 0.011 0.001 PHE A 282 TRP 0.004 0.001 TRP B 308 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00373 (13347) covalent geometry : angle 0.50739 (18153) SS BOND : bond 0.00371 ( 18) SS BOND : angle 1.00354 ( 36) hydrogen bonds : bond 0.03405 ( 537) hydrogen bonds : angle 4.73590 ( 1503) link_NAG-ASN : bond 0.00148 ( 12) link_NAG-ASN : angle 1.24403 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8365 (tt0) cc_final: 0.8119 (tm-30) REVERT: A 336 ARG cc_start: 0.8392 (ptm160) cc_final: 0.8187 (tpt-90) REVERT: E 40 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8442 (mtm-85) REVERT: E 104 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8350 (mp0) REVERT: B 220 ASP cc_start: 0.8483 (m-30) cc_final: 0.7964 (p0) REVERT: C 36 ILE cc_start: 0.8759 (tt) cc_final: 0.8494 (tt) REVERT: C 411 MET cc_start: 0.8941 (tmm) cc_final: 0.8688 (tmm) REVERT: G 79 ASN cc_start: 0.8510 (m-40) cc_final: 0.7192 (t0) outliers start: 25 outliers final: 14 residues processed: 149 average time/residue: 0.1165 time to fit residues: 25.3558 Evaluate side-chains 137 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 10 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.080539 restraints weight = 22627.021| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.21 r_work: 0.2964 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13377 Z= 0.099 Angle : 0.473 5.960 18225 Z= 0.246 Chirality : 0.045 0.174 2208 Planarity : 0.003 0.049 2286 Dihedral : 4.218 31.644 2034 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.07 % Allowed : 13.52 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1659 helix: 1.71 (0.24), residues: 471 sheet: 0.04 (0.26), residues: 399 loop : -1.11 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 353 TYR 0.009 0.001 TYR A 248 PHE 0.009 0.001 PHE C 282 TRP 0.004 0.001 TRP B 308 HIS 0.002 0.000 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00226 (13347) covalent geometry : angle 0.46885 (18153) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.90670 ( 36) hydrogen bonds : bond 0.03079 ( 537) hydrogen bonds : angle 4.58026 ( 1503) link_NAG-ASN : bond 0.00159 ( 12) link_NAG-ASN : angle 1.18950 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.551 Fit side-chains REVERT: A 196 GLU cc_start: 0.8303 (tt0) cc_final: 0.8085 (tm-30) REVERT: A 336 ARG cc_start: 0.8387 (ptm160) cc_final: 0.8184 (tpt-90) REVERT: E 104 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8354 (mp0) REVERT: B 220 ASP cc_start: 0.8379 (m-30) cc_final: 0.7909 (p0) REVERT: F 33 SER cc_start: 0.9227 (t) cc_final: 0.9005 (t) REVERT: C 36 ILE cc_start: 0.8727 (tt) cc_final: 0.8515 (tt) REVERT: C 411 MET cc_start: 0.8905 (tmm) cc_final: 0.8628 (tmm) REVERT: G 79 ASN cc_start: 0.8486 (m-40) cc_final: 0.7184 (t0) outliers start: 16 outliers final: 14 residues processed: 151 average time/residue: 0.1258 time to fit residues: 27.5018 Evaluate side-chains 137 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 0.0070 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 81 optimal weight: 0.0570 chunk 133 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.078891 restraints weight = 22525.227| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.19 r_work: 0.2936 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13377 Z= 0.143 Angle : 0.504 7.891 18225 Z= 0.259 Chirality : 0.045 0.167 2208 Planarity : 0.003 0.033 2286 Dihedral : 4.257 28.357 2034 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 13.19 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1659 helix: 1.73 (0.24), residues: 471 sheet: 0.27 (0.27), residues: 381 loop : -1.09 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 353 TYR 0.012 0.001 TYR A 248 PHE 0.011 0.001 PHE A 282 TRP 0.006 0.001 TRP G 77 HIS 0.002 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00338 (13347) covalent geometry : angle 0.50013 (18153) SS BOND : bond 0.00319 ( 18) SS BOND : angle 0.89828 ( 36) hydrogen bonds : bond 0.03246 ( 537) hydrogen bonds : angle 4.59901 ( 1503) link_NAG-ASN : bond 0.00125 ( 12) link_NAG-ASN : angle 1.20776 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8357 (tt0) cc_final: 0.8132 (tm-30) REVERT: E 104 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8360 (mp0) REVERT: B 220 ASP cc_start: 0.8394 (m-30) cc_final: 0.7974 (p0) REVERT: F 33 SER cc_start: 0.9214 (t) cc_final: 0.8984 (t) REVERT: C 36 ILE cc_start: 0.8770 (tt) cc_final: 0.8538 (tt) REVERT: G 79 ASN cc_start: 0.8445 (m-40) cc_final: 0.7230 (t0) outliers start: 24 outliers final: 19 residues processed: 144 average time/residue: 0.1208 time to fit residues: 25.4858 Evaluate side-chains 146 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 129 optimal weight: 0.0670 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078633 restraints weight = 22806.627| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.21 r_work: 0.2930 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13377 Z= 0.142 Angle : 0.502 7.607 18225 Z= 0.258 Chirality : 0.045 0.172 2208 Planarity : 0.003 0.030 2286 Dihedral : 4.244 21.958 2034 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.41 % Allowed : 13.65 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1659 helix: 1.66 (0.24), residues: 474 sheet: 0.26 (0.27), residues: 381 loop : -1.08 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 353 TYR 0.011 0.001 TYR A 248 PHE 0.010 0.001 PHE A 282 TRP 0.005 0.001 TRP G 77 HIS 0.002 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00336 (13347) covalent geometry : angle 0.49813 (18153) SS BOND : bond 0.00328 ( 18) SS BOND : angle 0.89449 ( 36) hydrogen bonds : bond 0.03255 ( 537) hydrogen bonds : angle 4.61409 ( 1503) link_NAG-ASN : bond 0.00120 ( 12) link_NAG-ASN : angle 1.22228 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.410 Fit side-chains REVERT: A 196 GLU cc_start: 0.8367 (tt0) cc_final: 0.8114 (tm-30) REVERT: E 104 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8350 (mp0) REVERT: B 220 ASP cc_start: 0.8401 (m-30) cc_final: 0.7826 (p0) REVERT: F 33 SER cc_start: 0.9217 (t) cc_final: 0.8990 (t) REVERT: F 47 GLU cc_start: 0.8631 (tt0) cc_final: 0.8368 (tt0) REVERT: C 36 ILE cc_start: 0.8752 (tt) cc_final: 0.8497 (tt) REVERT: C 411 MET cc_start: 0.8892 (tmm) cc_final: 0.8552 (tmm) REVERT: G 79 ASN cc_start: 0.8468 (m-40) cc_final: 0.7330 (t0) outliers start: 21 outliers final: 18 residues processed: 148 average time/residue: 0.1246 time to fit residues: 26.6594 Evaluate side-chains 148 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079481 restraints weight = 22720.758| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.21 r_work: 0.2945 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13377 Z= 0.120 Angle : 0.492 7.512 18225 Z= 0.253 Chirality : 0.045 0.174 2208 Planarity : 0.003 0.045 2286 Dihedral : 4.161 21.254 2034 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.27 % Allowed : 14.06 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1659 helix: 1.67 (0.24), residues: 474 sheet: 0.06 (0.26), residues: 399 loop : -1.11 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 353 TYR 0.010 0.001 TYR A 248 PHE 0.010 0.001 PHE B 282 TRP 0.006 0.001 TRP E 41 HIS 0.002 0.001 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00281 (13347) covalent geometry : angle 0.48814 (18153) SS BOND : bond 0.00278 ( 18) SS BOND : angle 0.82781 ( 36) hydrogen bonds : bond 0.03138 ( 537) hydrogen bonds : angle 4.58007 ( 1503) link_NAG-ASN : bond 0.00122 ( 12) link_NAG-ASN : angle 1.22352 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.495 Fit side-chains REVERT: A 196 GLU cc_start: 0.8356 (tt0) cc_final: 0.8105 (tm-30) REVERT: E 104 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8332 (mp0) REVERT: B 220 ASP cc_start: 0.8351 (m-30) cc_final: 0.7814 (p0) REVERT: F 33 SER cc_start: 0.9188 (t) cc_final: 0.8977 (t) REVERT: F 47 GLU cc_start: 0.8604 (tt0) cc_final: 0.8362 (tt0) REVERT: C 36 ILE cc_start: 0.8743 (tt) cc_final: 0.8502 (tt) REVERT: C 411 MET cc_start: 0.8867 (tmm) cc_final: 0.8533 (tmm) REVERT: G 79 ASN cc_start: 0.8448 (m-40) cc_final: 0.7382 (t0) outliers start: 19 outliers final: 18 residues processed: 151 average time/residue: 0.1257 time to fit residues: 27.4442 Evaluate side-chains 150 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN F 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.077086 restraints weight = 22830.738| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.19 r_work: 0.2899 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13377 Z= 0.188 Angle : 0.535 7.497 18225 Z= 0.275 Chirality : 0.046 0.182 2208 Planarity : 0.003 0.040 2286 Dihedral : 4.433 26.629 2034 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.41 % Allowed : 13.86 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1659 helix: 1.58 (0.24), residues: 474 sheet: 0.22 (0.26), residues: 390 loop : -1.15 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 353 TYR 0.014 0.001 TYR A 248 PHE 0.012 0.001 PHE A 282 TRP 0.005 0.001 TRP E 41 HIS 0.002 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00451 (13347) covalent geometry : angle 0.53169 (18153) SS BOND : bond 0.00400 ( 18) SS BOND : angle 0.94572 ( 36) hydrogen bonds : bond 0.03463 ( 537) hydrogen bonds : angle 4.72144 ( 1503) link_NAG-ASN : bond 0.00158 ( 12) link_NAG-ASN : angle 1.28487 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.38 seconds wall clock time: 53 minutes 47.61 seconds (3227.61 seconds total)