Starting phenix.real_space_refine on Wed Mar 4 19:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upd_26662/03_2026/7upd_26662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upd_26662/03_2026/7upd_26662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upd_26662/03_2026/7upd_26662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upd_26662/03_2026/7upd_26662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upd_26662/03_2026/7upd_26662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upd_26662/03_2026/7upd_26662.map" } resolution = 2.4 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= -0.001 sd= 0.245 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 96 5.16 5 C 10014 2.51 5 N 2574 2.21 5 O 3117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15801 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "D" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "F" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3395 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 1 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} 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: "D" 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: "G" 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: 3.37, per 1000 atoms: 0.21 Number of scatterers: 15801 At special positions: 0 Unit cell: (137.28, 132.66, 122.1, 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 96 16.00 O 3117 8.00 N 2574 7.00 C 10014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.04 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 501.0 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 30 sheets defined 30.7% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.727A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.713A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.950A pdb=" N THR A 168 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.681A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.676A 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 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.836A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 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 437 through 441 removed outlier: 3.514A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 474 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.641A pdb=" N THR B 31 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 52A through 54 Processing helix chain 'B' and resid 83 through 87 removed outlier: 4.016A pdb=" N THR B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.642A pdb=" N THR C 31 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 52A through 54 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.556A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.998A pdb=" N THR C 87 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 36 Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.690A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.716A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 137 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.653A pdb=" N LYS D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.962A pdb=" N THR D 168 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.674A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.826A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.506A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 474 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.827A pdb=" N LEU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.854A pdb=" N LEU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.727A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.735A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 137 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.639A pdb=" N LYS G 146 " --> pdb=" O ASP G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.955A pdb=" N THR G 168 " --> pdb=" O ALA G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 182 through 187 removed outlier: 3.675A pdb=" N THR G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.830A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.514A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 474 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.621A pdb=" N THR H 31 " --> pdb=" O ILE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.997A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.814A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.804A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.228A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY A 264 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 281 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE A 266 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG A 279 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 268 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 275 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.627A pdb=" N VAL G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (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 302 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 393 through 394 removed outlier: 3.614A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.117A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.117A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY B 96 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.121A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.121A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY C 96 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.811A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.195A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 9.360A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB8, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.611A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 425 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.490A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.496A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.803A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL G 338 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS G 45 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N CYS G 340 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS G 47 " --> pdb=" O CYS G 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.232A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY G 264 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR G 281 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE G 266 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG G 279 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 268 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR G 275 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.127A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLY H 96 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE H 100 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.493A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1755 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: 2.42 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5020 1.34 - 1.46: 3684 1.46 - 1.58: 7238 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 16086 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG G 503 " pdb=" O5 NAG G 503 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 ... (remaining 16081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 20990 1.26 - 2.52: 666 2.52 - 3.79: 133 3.79 - 5.05: 28 5.05 - 6.31: 11 Bond angle restraints: 21828 Sorted by residual: angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.79 118.29 4.50 1.78e+00 3.16e-01 6.39e+00 angle pdb=" C PRO A 191 " pdb=" N CYS A 192 " pdb=" CA CYS A 192 " ideal model delta sigma weight residual 122.56 118.24 4.32 1.72e+00 3.38e-01 6.29e+00 angle pdb=" C ILE E 48 " pdb=" N TYR E 49 " pdb=" CA TYR E 49 " ideal model delta sigma weight residual 122.79 118.35 4.44 1.78e+00 3.16e-01 6.21e+00 angle pdb=" C PRO G 191 " pdb=" N CYS G 192 " pdb=" CA CYS G 192 " ideal model delta sigma weight residual 122.56 118.29 4.27 1.72e+00 3.38e-01 6.16e+00 angle pdb=" C ILE F 48 " pdb=" N TYR F 49 " pdb=" CA TYR F 49 " ideal model delta sigma weight residual 122.79 118.48 4.31 1.78e+00 3.16e-01 5.87e+00 ... (remaining 21823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8825 17.98 - 35.95: 763 35.95 - 53.93: 243 53.93 - 71.90: 59 71.90 - 89.88: 19 Dihedral angle restraints: 9909 sinusoidal: 4026 harmonic: 5883 Sorted by residual: dihedral pdb=" CB CYS G 104 " pdb=" SG CYS G 104 " pdb=" SG CYS G 114 " pdb=" CB CYS G 114 " ideal model delta sinusoidal sigma weight residual 93.00 5.80 87.20 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 114 " pdb=" CB CYS A 114 " ideal model delta sinusoidal sigma weight residual -86.00 -0.92 -85.08 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS D 104 " pdb=" SG CYS D 104 " pdb=" SG CYS D 114 " pdb=" CB CYS D 114 " ideal model delta sinusoidal sigma weight residual -86.00 -6.37 -79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 9906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1507 0.032 - 0.065: 686 0.065 - 0.097: 217 0.097 - 0.130: 142 0.130 - 0.162: 22 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CA VAL A 312 " pdb=" N VAL A 312 " pdb=" C VAL A 312 " pdb=" CB VAL A 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" C1 NAG G 502 " pdb=" ND2 ASN G 99 " pdb=" C2 NAG G 502 " pdb=" O5 NAG G 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL G 312 " pdb=" N VAL G 312 " pdb=" C VAL G 312 " pdb=" CB VAL G 312 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2571 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 186 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C THR G 186 " 0.038 2.00e-02 2.50e+03 pdb=" O THR G 186 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE G 187 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 105 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" CD GLN B 105 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 105 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 105 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 31 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C THR B 31 " -0.028 2.00e-02 2.50e+03 pdb=" O THR B 31 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 32 " 0.010 2.00e-02 2.50e+03 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1735 2.76 - 3.29: 13976 3.29 - 3.83: 25669 3.83 - 4.36: 31371 4.36 - 4.90: 52973 Nonbonded interactions: 125724 Sorted by model distance: nonbonded pdb=" O TYR F 49 " pdb=" OH TYR F 91 " model vdw 2.222 3.040 nonbonded pdb=" O TYR L 49 " pdb=" OH TYR L 91 " model vdw 2.227 3.040 nonbonded pdb=" O TYR E 49 " pdb=" OH TYR E 91 " model vdw 2.231 3.040 nonbonded pdb=" NH2 ARG E 54 " pdb=" OD1 ASP E 60 " model vdw 2.302 3.120 nonbonded pdb=" NE2 HIS C 35 " pdb=" OE1 GLU C 95 " model vdw 2.401 3.120 ... (remaining 125719 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } 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: 13.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.003 0.031 16122 Z= 0.145 Angle : 0.574 6.310 21912 Z= 0.315 Chirality : 0.047 0.162 2574 Planarity : 0.004 0.038 2742 Dihedral : 15.736 89.880 6069 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 14.16 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.86 (0.19), residues: 1992 helix: 1.87 (0.25), residues: 435 sheet: 0.92 (0.20), residues: 642 loop : -0.28 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 54 TYR 0.019 0.001 TYR E 49 PHE 0.013 0.001 PHE G 301 TRP 0.008 0.001 TRP L 50 HIS 0.006 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00283 (16086) covalent geometry : angle 0.56851 (21828) SS BOND : bond 0.00482 ( 24) SS BOND : angle 1.26345 ( 48) hydrogen bonds : bond 0.13966 ( 655) hydrogen bonds : angle 6.21734 ( 1755) link_NAG-ASN : bond 0.00225 ( 12) link_NAG-ASN : angle 1.45922 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.623 Fit side-chains REVERT: C 105 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8145 (mm110) outliers start: 21 outliers final: 18 residues processed: 268 average time/residue: 0.5949 time to fit residues: 175.9710 Evaluate side-chains 259 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 342 GLN Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN G 465 GLN H 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099556 restraints weight = 17372.357| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.72 r_work: 0.3042 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16122 Z= 0.111 Angle : 0.505 4.820 21912 Z= 0.278 Chirality : 0.045 0.179 2574 Planarity : 0.004 0.037 2742 Dihedral : 6.439 58.569 2444 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.72 % Allowed : 12.41 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1992 helix: 2.29 (0.26), residues: 441 sheet: 0.91 (0.20), residues: 645 loop : -0.15 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.019 0.001 TYR L 49 PHE 0.012 0.001 PHE D 301 TRP 0.008 0.001 TRP E 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00232 (16086) covalent geometry : angle 0.49948 (21828) SS BOND : bond 0.00495 ( 24) SS BOND : angle 1.09830 ( 48) hydrogen bonds : bond 0.04555 ( 655) hydrogen bonds : angle 5.09646 ( 1755) link_NAG-ASN : bond 0.00160 ( 12) link_NAG-ASN : angle 1.45660 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 256 time to evaluate : 0.538 Fit side-chains REVERT: A 139 LYS cc_start: 0.8499 (mptp) cc_final: 0.8293 (mmtm) REVERT: A 240 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: A 390 VAL cc_start: 0.8795 (p) cc_final: 0.8542 (t) REVERT: B 3 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: C 3 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8139 (tp40) REVERT: D 258 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: F 103 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8246 (tmtp) REVERT: G 258 GLU cc_start: 0.8358 (tp30) cc_final: 0.8067 (mp0) REVERT: G 336 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8403 (mtp180) REVERT: H 3 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8233 (tp40) REVERT: H 82 MET cc_start: 0.8490 (mtm) cc_final: 0.8246 (mtm) outliers start: 66 outliers final: 28 residues processed: 297 average time/residue: 0.5699 time to fit residues: 187.4997 Evaluate side-chains 281 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 342 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN D 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096600 restraints weight = 17539.071| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.74 r_work: 0.2994 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16122 Z= 0.140 Angle : 0.566 5.216 21912 Z= 0.312 Chirality : 0.048 0.184 2574 Planarity : 0.004 0.037 2742 Dihedral : 6.240 51.931 2439 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.61 % Allowed : 12.75 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1992 helix: 2.32 (0.26), residues: 441 sheet: 0.77 (0.20), residues: 606 loop : -0.11 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 319 TYR 0.023 0.002 TYR L 49 PHE 0.013 0.001 PHE D 301 TRP 0.011 0.002 TRP F 50 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00308 (16086) covalent geometry : angle 0.55929 (21828) SS BOND : bond 0.00680 ( 24) SS BOND : angle 1.47131 ( 48) hydrogen bonds : bond 0.05337 ( 655) hydrogen bonds : angle 5.11587 ( 1755) link_NAG-ASN : bond 0.00144 ( 12) link_NAG-ASN : angle 1.66374 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 0.635 Fit side-chains REVERT: A 139 LYS cc_start: 0.8508 (mptp) cc_final: 0.8287 (mmtm) REVERT: A 410 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 3 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8163 (tp40) REVERT: C 3 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8163 (tp40) REVERT: C 105 GLN cc_start: 0.8550 (mm110) cc_final: 0.8345 (mm110) REVERT: D 258 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: D 350 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (t0) REVERT: E 27 GLN cc_start: 0.8153 (mt0) cc_final: 0.7887 (mt0) REVERT: F 103 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8278 (tmtp) REVERT: G 152 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: G 336 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8461 (mtp180) REVERT: G 468 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: H 3 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8247 (tp40) REVERT: L 55 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7682 (tp30) outliers start: 64 outliers final: 24 residues processed: 286 average time/residue: 0.5964 time to fit residues: 188.5984 Evaluate side-chains 277 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN C 30 ASN D 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096265 restraints weight = 17364.716| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.72 r_work: 0.2989 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16122 Z= 0.143 Angle : 0.568 5.690 21912 Z= 0.313 Chirality : 0.048 0.185 2574 Planarity : 0.004 0.036 2742 Dihedral : 5.960 51.747 2435 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.44 % Allowed : 13.65 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.96 (0.19), residues: 1992 helix: 2.35 (0.26), residues: 438 sheet: 0.74 (0.20), residues: 621 loop : -0.23 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 279 TYR 0.023 0.002 TYR L 49 PHE 0.013 0.001 PHE D 301 TRP 0.012 0.002 TRP F 50 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00317 (16086) covalent geometry : angle 0.56110 (21828) SS BOND : bond 0.00708 ( 24) SS BOND : angle 1.45171 ( 48) hydrogen bonds : bond 0.05291 ( 655) hydrogen bonds : angle 5.09897 ( 1755) link_NAG-ASN : bond 0.00154 ( 12) link_NAG-ASN : angle 1.67589 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.618 Fit side-chains REVERT: A 139 LYS cc_start: 0.8528 (mptp) cc_final: 0.8306 (mmtm) REVERT: A 152 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: B 3 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8174 (tp40) REVERT: C 3 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8159 (tp40) REVERT: D 71 CYS cc_start: 0.3870 (OUTLIER) cc_final: 0.3472 (t) REVERT: D 258 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: F 103 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (tmtp) REVERT: G 139 LYS cc_start: 0.8435 (mptp) cc_final: 0.8225 (mmtm) REVERT: G 152 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: G 336 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8432 (mtp180) REVERT: G 468 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6058 (mp10) REVERT: H 3 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8267 (tp40) outliers start: 61 outliers final: 25 residues processed: 279 average time/residue: 0.6160 time to fit residues: 189.8065 Evaluate side-chains 268 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 50 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN C 105 GLN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097213 restraints weight = 17292.961| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.72 r_work: 0.3005 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16122 Z= 0.123 Angle : 0.535 5.547 21912 Z= 0.294 Chirality : 0.046 0.183 2574 Planarity : 0.004 0.035 2742 Dihedral : 5.685 51.391 2430 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.38 % Allowed : 13.82 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.97 (0.19), residues: 1992 helix: 2.43 (0.26), residues: 438 sheet: 0.69 (0.20), residues: 606 loop : -0.20 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.022 0.001 TYR L 49 PHE 0.012 0.001 PHE D 301 TRP 0.010 0.001 TRP F 50 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00265 (16086) covalent geometry : angle 0.52713 (21828) SS BOND : bond 0.00586 ( 24) SS BOND : angle 1.44218 ( 48) hydrogen bonds : bond 0.04842 ( 655) hydrogen bonds : angle 4.96819 ( 1755) link_NAG-ASN : bond 0.00148 ( 12) link_NAG-ASN : angle 1.65518 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.624 Fit side-chains REVERT: A 71 CYS cc_start: 0.3901 (OUTLIER) cc_final: 0.3581 (t) REVERT: A 152 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: B 3 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8172 (tp40) REVERT: C 3 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: C 105 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8328 (mm110) REVERT: D 258 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: D 336 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8477 (mtp180) REVERT: D 350 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8341 (t0) REVERT: E 103 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8243 (tmtp) REVERT: F 103 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (tmtp) REVERT: G 71 CYS cc_start: 0.3549 (OUTLIER) cc_final: 0.3297 (t) REVERT: G 139 LYS cc_start: 0.8425 (mptp) cc_final: 0.8217 (mmtm) REVERT: G 152 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: G 336 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8440 (mtp180) REVERT: H 3 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8253 (tp40) outliers start: 60 outliers final: 25 residues processed: 272 average time/residue: 0.6252 time to fit residues: 187.4539 Evaluate side-chains 268 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 336 ARG Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN G 465 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094659 restraints weight = 17246.202| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.72 r_work: 0.2966 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16122 Z= 0.177 Angle : 0.630 6.396 21912 Z= 0.345 Chirality : 0.050 0.200 2574 Planarity : 0.005 0.045 2742 Dihedral : 5.953 51.934 2430 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.55 % Allowed : 13.82 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.83 (0.18), residues: 1992 helix: 2.25 (0.26), residues: 441 sheet: 0.60 (0.20), residues: 621 loop : -0.27 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 319 TYR 0.025 0.002 TYR L 49 PHE 0.014 0.002 PHE A 301 TRP 0.014 0.002 TRP F 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00407 (16086) covalent geometry : angle 0.62158 (21828) SS BOND : bond 0.00857 ( 24) SS BOND : angle 1.78453 ( 48) hydrogen bonds : bond 0.05926 ( 655) hydrogen bonds : angle 5.20467 ( 1755) link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 1.77742 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 0.620 Fit side-chains REVERT: A 152 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: B 3 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: C 3 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (tp40) REVERT: D 258 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: D 336 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8518 (mtp180) REVERT: D 350 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8363 (t0) REVERT: D 410 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8656 (mp) REVERT: E 103 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8253 (tttp) REVERT: G 139 LYS cc_start: 0.8452 (mptp) cc_final: 0.8247 (mmtm) REVERT: G 152 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: G 468 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6140 (mp10) REVERT: H 3 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8277 (tp40) outliers start: 63 outliers final: 29 residues processed: 278 average time/residue: 0.6079 time to fit residues: 186.6603 Evaluate side-chains 278 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 0.1980 chunk 186 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098481 restraints weight = 17390.246| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.71 r_work: 0.3025 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16122 Z= 0.100 Angle : 0.493 5.987 21912 Z= 0.269 Chirality : 0.044 0.180 2574 Planarity : 0.004 0.036 2742 Dihedral : 5.401 50.890 2428 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.88 % Allowed : 14.21 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1992 helix: 2.53 (0.26), residues: 438 sheet: 0.68 (0.20), residues: 606 loop : -0.20 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.020 0.001 TYR L 49 PHE 0.010 0.001 PHE G 301 TRP 0.008 0.001 TRP E 50 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00199 (16086) covalent geometry : angle 0.48613 (21828) SS BOND : bond 0.00386 ( 24) SS BOND : angle 1.09032 ( 48) hydrogen bonds : bond 0.04209 ( 655) hydrogen bonds : angle 4.82347 ( 1755) link_NAG-ASN : bond 0.00090 ( 12) link_NAG-ASN : angle 1.69029 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.615 Fit side-chains REVERT: A 152 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: B 3 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8145 (tp40) REVERT: C 3 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (tp40) REVERT: D 258 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: D 350 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8327 (t0) REVERT: E 103 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8234 (tmtp) REVERT: G 152 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: H 3 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8223 (tp40) outliers start: 51 outliers final: 26 residues processed: 272 average time/residue: 0.6186 time to fit residues: 185.4915 Evaluate side-chains 273 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN C 105 GLN D 465 GLN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096765 restraints weight = 17425.015| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.72 r_work: 0.2997 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16122 Z= 0.128 Angle : 0.548 6.001 21912 Z= 0.299 Chirality : 0.046 0.181 2574 Planarity : 0.004 0.048 2742 Dihedral : 5.502 51.522 2428 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.76 % Allowed : 14.61 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1992 helix: 2.53 (0.26), residues: 441 sheet: 0.65 (0.20), residues: 606 loop : -0.17 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.023 0.001 TYR L 49 PHE 0.012 0.001 PHE A 301 TRP 0.010 0.001 TRP F 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00277 (16086) covalent geometry : angle 0.53976 (21828) SS BOND : bond 0.00620 ( 24) SS BOND : angle 1.52152 ( 48) hydrogen bonds : bond 0.04846 ( 655) hydrogen bonds : angle 4.90065 ( 1755) link_NAG-ASN : bond 0.00128 ( 12) link_NAG-ASN : angle 1.70584 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.637 Fit side-chains REVERT: A 152 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 3 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8149 (tp40) REVERT: C 3 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (tp40) REVERT: C 105 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8357 (mm110) REVERT: D 258 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8112 (tp30) REVERT: D 350 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8337 (t0) REVERT: E 103 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8232 (tttp) REVERT: G 152 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: H 3 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8253 (tp40) outliers start: 49 outliers final: 30 residues processed: 269 average time/residue: 0.6047 time to fit residues: 179.9452 Evaluate side-chains 276 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 24 LYS Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN G 102 HIS G 465 GLN H 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093545 restraints weight = 17255.588| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.71 r_work: 0.2949 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16122 Z= 0.214 Angle : 0.691 7.026 21912 Z= 0.379 Chirality : 0.052 0.219 2574 Planarity : 0.005 0.061 2742 Dihedral : 5.994 52.086 2428 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.54 % Allowed : 14.78 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.80 (0.18), residues: 1992 helix: 2.07 (0.25), residues: 456 sheet: 0.54 (0.20), residues: 621 loop : -0.19 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 279 TYR 0.026 0.002 TYR L 49 PHE 0.015 0.002 PHE A 301 TRP 0.016 0.003 TRP L 50 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00500 (16086) covalent geometry : angle 0.68277 (21828) SS BOND : bond 0.01063 ( 24) SS BOND : angle 1.83673 ( 48) hydrogen bonds : bond 0.06481 ( 655) hydrogen bonds : angle 5.30328 ( 1755) link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 1.93796 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.613 Fit side-chains REVERT: A 152 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: B 3 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8203 (tp40) REVERT: C 3 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8181 (tp40) REVERT: C 105 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8406 (mm110) REVERT: D 258 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: D 350 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8380 (t0) REVERT: E 27 GLN cc_start: 0.8171 (mt0) cc_final: 0.7915 (mt0) REVERT: E 103 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8230 (tttp) REVERT: G 139 LYS cc_start: 0.8477 (mptp) cc_final: 0.8271 (mmtm) REVERT: G 152 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: H 3 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8260 (tp40) outliers start: 45 outliers final: 32 residues processed: 270 average time/residue: 0.6215 time to fit residues: 184.7503 Evaluate side-chains 279 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 0.0370 chunk 19 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN G 465 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094707 restraints weight = 17322.762| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.71 r_work: 0.2967 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16122 Z= 0.164 Angle : 0.622 6.453 21912 Z= 0.340 Chirality : 0.049 0.188 2574 Planarity : 0.004 0.044 2742 Dihedral : 5.848 51.513 2428 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.59 % Allowed : 14.78 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.18), residues: 1992 helix: 2.29 (0.26), residues: 438 sheet: 0.51 (0.20), residues: 621 loop : -0.30 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.023 0.002 TYR L 49 PHE 0.013 0.001 PHE D 301 TRP 0.014 0.002 TRP L 50 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (16086) covalent geometry : angle 0.61427 (21828) SS BOND : bond 0.00806 ( 24) SS BOND : angle 1.58572 ( 48) hydrogen bonds : bond 0.05691 ( 655) hydrogen bonds : angle 5.16479 ( 1755) link_NAG-ASN : bond 0.00175 ( 12) link_NAG-ASN : angle 1.89415 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.620 Fit side-chains REVERT: A 152 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: B 3 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8176 (tp40) REVERT: C 3 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8171 (tp40) REVERT: C 105 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8405 (mm110) REVERT: D 258 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: D 350 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8360 (t0) REVERT: E 103 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8205 (tttp) REVERT: G 139 LYS cc_start: 0.8468 (mptp) cc_final: 0.8260 (mmtm) REVERT: G 152 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: H 3 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8248 (tp40) outliers start: 46 outliers final: 31 residues processed: 265 average time/residue: 0.5871 time to fit residues: 171.8891 Evaluate side-chains 275 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 192 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN B 105 GLN C 30 ASN G 465 GLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099466 restraints weight = 17509.265| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.72 r_work: 0.3042 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16122 Z= 0.098 Angle : 0.488 6.115 21912 Z= 0.265 Chirality : 0.044 0.172 2574 Planarity : 0.004 0.038 2742 Dihedral : 5.317 51.064 2428 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.14 % Allowed : 15.17 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 1992 helix: 2.57 (0.26), residues: 438 sheet: 0.69 (0.20), residues: 600 loop : -0.22 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 244 TYR 0.018 0.001 TYR F 49 PHE 0.011 0.001 PHE D 301 TRP 0.006 0.001 TRP C 36 HIS 0.003 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00193 (16086) covalent geometry : angle 0.48158 (21828) SS BOND : bond 0.00368 ( 24) SS BOND : angle 1.06551 ( 48) hydrogen bonds : bond 0.03833 ( 655) hydrogen bonds : angle 4.70255 ( 1755) link_NAG-ASN : bond 0.00133 ( 12) link_NAG-ASN : angle 1.71640 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6901.23 seconds wall clock time: 117 minutes 56.47 seconds (7076.47 seconds total)