Starting phenix.real_space_refine on Fri Aug 7 04:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10fi_75131/08_2026/10fi_75131.cif Found real_map, /net/cci-nas-00/data/ceres_data/10fi_75131/08_2026/10fi_75131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10fi_75131/08_2026/10fi_75131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10fi_75131/08_2026/10fi_75131.map" model { file = "/net/cci-nas-00/data/ceres_data/10fi_75131/08_2026/10fi_75131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10fi_75131/08_2026/10fi_75131.cif" } resolution = 3.3 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= 0.027 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 78 5.16 5 C 12067 2.51 5 N 3267 2.21 5 O 3418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18830 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1037 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 130} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "I" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3364 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 400} Chain: "K" Number of atoms: 854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 843 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Conformer: "B" Number of residues, atoms: 114, 843 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 bond proxies already assigned to first conformer: 839 Chain: "L" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1937 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2929 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 8, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 71 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1865 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 92 Chain: "Q" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1421 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 15, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "U" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1229 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 11, 'PHE:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 15, 'TYR:plan': 1, 'GLU:plan': 16, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 4.24, per 1000 atoms: 0.23 Number of scatterers: 18830 At special positions: 0 Unit cell: (117.7, 186.18, 166.92, 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 78 16.00 O 3418 8.00 N 3267 7.00 C 12067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 879.8 milliseconds 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 11 sheets defined 63.8% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 4 through 38 removed outlier: 4.015A pdb=" N GLN H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU H 21 " --> pdb=" O LYS H 17 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 Processing helix chain 'H' and resid 50 through 73 Processing helix chain 'H' and resid 82 through 93 removed outlier: 4.509A pdb=" N ASN H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 135 removed outlier: 3.504A pdb=" N GLU H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 338 removed outlier: 4.262A pdb=" N HIS I 338 " --> pdb=" O SER I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 348 Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 374 through 388 removed outlier: 3.880A pdb=" N VAL I 378 " --> pdb=" O THR I 374 " (cutoff:3.500A) Proline residue: I 380 - end of helix removed outlier: 3.868A pdb=" N MET I 388 " --> pdb=" O SER I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 401 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.557A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 450 removed outlier: 4.292A pdb=" N ASP I 450 " --> pdb=" O TRP I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 474 removed outlier: 3.545A pdb=" N LEU I 474 " --> pdb=" O THR I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 Processing helix chain 'I' and resid 506 through 524 Processing helix chain 'I' and resid 538 through 547 removed outlier: 3.649A pdb=" N SER I 547 " --> pdb=" O ASN I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 566 removed outlier: 4.263A pdb=" N ASN I 566 " --> pdb=" O VAL I 562 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 593 Processing helix chain 'I' and resid 607 through 619 removed outlier: 3.755A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR I 619 " --> pdb=" O LEU I 615 " (cutoff:3.500A) Processing helix chain 'I' and resid 626 through 630 removed outlier: 3.999A pdb=" N LYS I 629 " --> pdb=" O LYS I 626 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE I 630 " --> pdb=" O ASN I 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 626 through 630' Processing helix chain 'I' and resid 631 through 636 removed outlier: 3.545A pdb=" N ILE I 636 " --> pdb=" O THR I 632 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 654 Processing helix chain 'I' and resid 666 through 677 Processing helix chain 'I' and resid 677 through 685 Processing helix chain 'I' and resid 692 through 707 Processing helix chain 'I' and resid 711 through 722 removed outlier: 3.973A pdb=" N ALA I 715 " --> pdb=" O TYR I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 725 through 729 Processing helix chain 'K' and resid 8 through 41 removed outlier: 3.568A pdb=" N ILE K 12 " --> pdb=" O LEU K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 53 through 58 removed outlier: 3.552A pdb=" N ARG K 58 " --> pdb=" O THR K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 127 removed outlier: 3.872A pdb=" N ASP K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 100 " --> pdb=" O GLN K 96 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE K 127 " --> pdb=" O HIS K 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.691A pdb=" N VAL L 98 " --> pdb=" O ASN L 94 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 128 removed outlier: 3.534A pdb=" N ILE L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 187 through 197 Processing helix chain 'L' and resid 229 through 240 Processing helix chain 'N' and resid 16 through 25 removed outlier: 3.609A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.547A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 64 Processing helix chain 'N' and resid 67 through 78 removed outlier: 4.006A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.838A pdb=" N PHE N 104 " --> pdb=" O PRO N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 124 through 138 removed outlier: 3.514A pdb=" N ILE N 129 " --> pdb=" O PRO N 125 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 234 removed outlier: 4.527A pdb=" N SER N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU N 234 " --> pdb=" O ARG N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 Processing helix chain 'N' and resid 261 through 265 removed outlier: 3.615A pdb=" N ALA N 264 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 261 through 265' Processing helix chain 'N' and resid 270 through 276 removed outlier: 3.608A pdb=" N ALA N 274 " --> pdb=" O TRP N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 257 Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.506A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 348 removed outlier: 3.855A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 363 removed outlier: 3.513A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN O 360 " --> pdb=" O GLU O 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS O 361 " --> pdb=" O LEU O 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 110 Processing helix chain 'P' and resid 133 through 140 Processing helix chain 'P' and resid 149 through 160 Processing helix chain 'P' and resid 224 through 233 removed outlier: 4.127A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA P 233 " --> pdb=" O LYS P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 266 Processing helix chain 'P' and resid 333 through 349 removed outlier: 3.558A pdb=" N LEU P 337 " --> pdb=" O ASN P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 363 removed outlier: 3.753A pdb=" N LYS P 355 " --> pdb=" O LYS P 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 184 removed outlier: 3.539A pdb=" N GLU Q 184 " --> pdb=" O LYS Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 219 removed outlier: 3.614A pdb=" N ILE Q 199 " --> pdb=" O GLU Q 195 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR Q 200 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 292 Processing helix chain 'Q' and resid 321 through 333 removed outlier: 4.053A pdb=" N PHE Q 325 " --> pdb=" O GLY Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 3.991A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET Q 377 " --> pdb=" O THR Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 391 Processing helix chain 'U' and resid 132 through 155 Proline residue: U 152 - end of helix Processing helix chain 'U' and resid 167 through 232 removed outlier: 3.828A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU U 175 " --> pdb=" O TYR U 171 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 319 Processing helix chain 'Y' and resid 3 through 16 Processing helix chain 'Y' and resid 16 through 22 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 55 through 83 removed outlier: 3.746A pdb=" N GLN Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU Y 83 " --> pdb=" O GLN Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 103 Processing helix chain 'Y' and resid 109 through 117 Processing helix chain 'Y' and resid 137 through 186 Processing helix chain 'Y' and resid 189 through 219 removed outlier: 4.750A pdb=" N ASN Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLY Y 199 " --> pdb=" O ALA Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 238 removed outlier: 3.675A pdb=" N LYS Y 238 " --> pdb=" O SER Y 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 14 removed outlier: 3.652A pdb=" N SER Z 14 " --> pdb=" O TYR Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 24 removed outlier: 3.935A pdb=" N SER Z 21 " --> pdb=" O THR Z 17 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE Z 22 " --> pdb=" O THR Z 18 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 41 removed outlier: 4.136A pdb=" N HIS Z 41 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 37 through 41' Processing helix chain 'Z' and resid 43 through 84 removed outlier: 3.757A pdb=" N GLN Z 47 " --> pdb=" O TYR Z 43 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Z 48 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 127 removed outlier: 3.568A pdb=" N MET Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 153 Processing sheet with id=AA1, first strand: chain 'L' and resid 32 through 36 removed outlier: 3.921A pdb=" N ASP L 34 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU L 57 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP L 112 " --> pdb=" O GLY L 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 32 through 36 removed outlier: 3.921A pdb=" N ASP L 34 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU L 57 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR L 3 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR L 148 " --> pdb=" O THR L 206 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL L 208 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS L 146 " --> pdb=" O VAL L 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL N 385 " --> pdb=" O PHE N 404 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE N 442 " --> pdb=" O GLY N 386 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR N 388 " --> pdb=" O ILE N 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'N' and resid 117 through 118 removed outlier: 3.911A pdb=" N LYS N 117 " --> pdb=" O ARG N 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG N 113 " --> pdb=" O LYS N 117 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 141 through 148 removed outlier: 4.146A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 295 through 298 Processing sheet with id=AA7, first strand: chain 'O' and resid 175 through 180 removed outlier: 4.235A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 297 through 298 Processing sheet with id=AA9, first strand: chain 'P' and resid 165 through 175 removed outlier: 3.634A pdb=" N ASN P 186 " --> pdb=" O SER P 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG P 172 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL P 182 " --> pdb=" O ARG P 172 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG P 174 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE P 180 " --> pdb=" O ARG P 174 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU P 181 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU P 198 " --> pdb=" O ARG P 219 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG P 219 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN P 200 " --> pdb=" O ILE P 217 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE P 217 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS P 202 " --> pdb=" O TRP P 215 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP P 215 " --> pdb=" O LYS P 202 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE P 204 " --> pdb=" O LEU P 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 270 through 272 Processing sheet with id=AB2, first strand: chain 'P' and resid 301 through 303 removed outlier: 6.529A pdb=" N SER P 319 " --> pdb=" O MET Q 335 " (cutoff:3.500A) 1286 hydrogen bonds defined for protein. 3783 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: 3.59 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6099 1.34 - 1.46: 3750 1.46 - 1.58: 9147 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 19125 Sorted by residual: bond pdb=" CA ASN K 77 " pdb=" CB ASN K 77 " ideal model delta sigma weight residual 1.530 1.569 -0.039 1.58e-02 4.01e+03 5.99e+00 bond pdb=" CA LEU L 26 " pdb=" C LEU L 26 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.40e-02 5.10e+03 2.73e+00 bond pdb=" CA SER K 76 " pdb=" CB SER K 76 " ideal model delta sigma weight residual 1.528 1.554 -0.025 1.59e-02 3.96e+03 2.57e+00 bond pdb=" C LYS H 75 " pdb=" N PRO H 76 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.19e+00 bond pdb=" N MET K 61 " pdb=" CA MET K 61 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.89e+00 ... (remaining 19120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 25639 3.01 - 6.02: 192 6.02 - 9.03: 40 9.03 - 12.04: 6 12.04 - 15.05: 1 Bond angle restraints: 25878 Sorted by residual: angle pdb=" CA LEU I 701 " pdb=" CB LEU I 701 " pdb=" CG LEU I 701 " ideal model delta sigma weight residual 116.30 131.35 -15.05 3.50e+00 8.16e-02 1.85e+01 angle pdb=" N LEU U 305 " pdb=" CA LEU U 305 " pdb=" C LEU U 305 " ideal model delta sigma weight residual 113.43 108.25 5.18 1.26e+00 6.30e-01 1.69e+01 angle pdb=" N PRO K 60 " pdb=" CA PRO K 60 " pdb=" C PRO K 60 " ideal model delta sigma weight residual 112.47 120.74 -8.27 2.06e+00 2.36e-01 1.61e+01 angle pdb=" C GLN L 25 " pdb=" N LEU L 26 " pdb=" CA LEU L 26 " ideal model delta sigma weight residual 122.54 116.15 6.39 1.65e+00 3.67e-01 1.50e+01 angle pdb=" CA MET Z 125 " pdb=" CB MET Z 125 " pdb=" CG MET Z 125 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 ... (remaining 25873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10060 17.94 - 35.88: 1244 35.88 - 53.83: 300 53.83 - 71.77: 45 71.77 - 89.71: 13 Dihedral angle restraints: 11662 sinusoidal: 4402 harmonic: 7260 Sorted by residual: dihedral pdb=" CA VAL L 40 " pdb=" C VAL L 40 " pdb=" N PRO L 41 " pdb=" CA PRO L 41 " ideal model delta harmonic sigma weight residual -180.00 -138.11 -41.89 0 5.00e+00 4.00e-02 7.02e+01 dihedral pdb=" CA LYS H 75 " pdb=" C LYS H 75 " pdb=" N PRO H 76 " pdb=" CA PRO H 76 " ideal model delta harmonic sigma weight residual 180.00 -141.14 -38.86 0 5.00e+00 4.00e-02 6.04e+01 dihedral pdb=" CA LYS K 59 " pdb=" C LYS K 59 " pdb=" N PRO K 60 " pdb=" CA PRO K 60 " ideal model delta harmonic sigma weight residual -180.00 -142.04 -37.96 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 11659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2318 0.043 - 0.086: 609 0.086 - 0.129: 143 0.129 - 0.173: 19 0.173 - 0.216: 2 Chirality restraints: 3091 Sorted by residual: chirality pdb=" CA PRO K 60 " pdb=" N PRO K 60 " pdb=" C PRO K 60 " pdb=" CB PRO K 60 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE H 12 " pdb=" CA ILE H 12 " pdb=" CG1 ILE H 12 " pdb=" CG2 ILE H 12 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE H 55 " pdb=" CA ILE H 55 " pdb=" CG1 ILE H 55 " pdb=" CG2 ILE H 55 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 3088 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 75 " 0.084 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO H 76 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 77 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" CG ASN K 77 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN K 77 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN K 77 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 25 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C GLN L 25 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN L 25 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU L 26 " 0.014 2.00e-02 2.50e+03 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 261 2.66 - 3.22: 18293 3.22 - 3.78: 30272 3.78 - 4.34: 37632 4.34 - 4.90: 62912 Nonbonded interactions: 149370 Sorted by model distance: nonbonded pdb=" O ARG U 176 " pdb=" OG1 THR U 180 " model vdw 2.102 3.040 nonbonded pdb=" O THR H 84 " pdb=" ND2 ASN H 88 " model vdw 2.177 3.120 nonbonded pdb=" O PRO I 422 " pdb=" ND2 ASN I 471 " model vdw 2.193 3.120 nonbonded pdb=" O SER I 447 " pdb=" ND2 ASN I 455 " model vdw 2.220 3.120 nonbonded pdb=" OG SER Q 359 " pdb=" OD1 ASP Z 109 " model vdw 2.239 3.040 ... (remaining 149365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 5.070 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.004 0.040 19125 Z= 0.164 Angle : 0.719 15.053 25878 Z= 0.372 Chirality : 0.041 0.216 3091 Planarity : 0.004 0.129 3251 Dihedral : 16.746 89.712 6904 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 1.95 % Allowed : 28.85 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.48 % 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: 1.43 (0.18), residues: 2401 helix: 2.21 (0.14), residues: 1422 sheet: -0.21 (0.36), residues: 229 loop : -1.21 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 74 TYR 0.020 0.001 TYR Y 5 PHE 0.026 0.002 PHE N 104 TRP 0.026 0.002 TRP K 89 HIS 0.014 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (19125) covalent geometry : angle 0.71880 / 0.37 (25878) hydrogen bonds : bond 0.13633 / 8.97 ( 1254) hydrogen bonds : angle 6.04206 / 4.40 ( 3783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7758 (mp-120) REVERT: H 15 LEU cc_start: 0.8821 (mt) cc_final: 0.8501 (mt) REVERT: H 102 GLN cc_start: 0.8573 (pp30) cc_final: 0.8328 (pp30) REVERT: I 445 MET cc_start: 0.8199 (mmm) cc_final: 0.7881 (mmm) REVERT: I 446 TRP cc_start: 0.8135 (t-100) cc_final: 0.7673 (t-100) REVERT: I 510 MET cc_start: 0.8983 (mpp) cc_final: 0.8310 (mpp) REVERT: K 57 LEU cc_start: 0.7774 (pp) cc_final: 0.7253 (tt) REVERT: L 25 GLN cc_start: 0.8090 (mt0) cc_final: 0.7526 (mp10) REVERT: L 97 GLU cc_start: 0.7284 (mp0) cc_final: 0.7022 (mp0) REVERT: L 101 GLN cc_start: 0.8143 (mm110) cc_final: 0.7676 (mm-40) REVERT: N 195 ILE cc_start: 0.8340 (tt) cc_final: 0.7539 (mp) REVERT: N 271 GLU cc_start: 0.8651 (tt0) cc_final: 0.8321 (mt-10) REVERT: O 305 MET cc_start: 0.8534 (mmm) cc_final: 0.8186 (mmt) REVERT: O 322 ASN cc_start: 0.8020 (t0) cc_final: 0.7818 (t0) REVERT: O 345 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6635 (mt-10) REVERT: P 274 MET cc_start: 0.7999 (tpp) cc_final: 0.7764 (tpt) REVERT: Q 335 MET cc_start: 0.8334 (ptp) cc_final: 0.7992 (ptt) REVERT: U 185 MET cc_start: 0.8907 (mmt) cc_final: 0.8374 (mmm) REVERT: U 190 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8168 (mmmm) REVERT: U 219 GLN cc_start: 0.9053 (tt0) cc_final: 0.8784 (mt0) REVERT: U 258 ASP cc_start: 0.7967 (m-30) cc_final: 0.7689 (t70) REVERT: Y 104 GLU cc_start: 0.7300 (tp30) cc_final: 0.6511 (pp20) REVERT: Y 138 LYS cc_start: 0.7131 (pttm) cc_final: 0.6233 (tmmt) REVERT: Y 145 ASN cc_start: 0.8728 (t0) cc_final: 0.8520 (m-40) REVERT: Z 42 TRP cc_start: 0.5246 (t-100) cc_final: 0.4862 (t-100) REVERT: Z 102 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8403 (tp-100) outliers start: 38 outliers final: 31 residues processed: 317 average time/residue: 0.1456 time to fit residues: 71.4861 Evaluate side-chains 289 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 569 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 296 ASP Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 217 ILE Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 352 THR Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain Y residue 17 THR Chi-restraints excluded: chain Y residue 102 GLU Chi-restraints excluded: chain Y residue 176 SER Chi-restraints excluded: chain Z residue 65 PHE Chi-restraints excluded: chain Z residue 102 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN K 107 GLN N 23 GLN O 283 GLN Q 246 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.126467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093936 restraints weight = 41428.593| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.54 r_work: 0.3259 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19125 Z= 0.146 Angle : 0.601 9.053 25878 Z= 0.306 Chirality : 0.040 0.207 3091 Planarity : 0.004 0.116 3251 Dihedral : 5.879 64.597 2671 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 4.11 % Allowed : 23.67 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.48 % 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: 1.64 (0.18), residues: 2401 helix: 2.42 (0.14), residues: 1429 sheet: -0.14 (0.34), residues: 246 loop : -1.26 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 23 TYR 0.022 0.001 TYR Y 91 PHE 0.020 0.002 PHE Q 325 TRP 0.020 0.002 TRP K 89 HIS 0.008 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (19125) covalent geometry : angle 0.60127 / 0.31 (25878) hydrogen bonds : bond 0.04138 / 2.81 ( 1254) hydrogen bonds : angle 4.46660 / 3.21 ( 3783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 283 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7840 (mp-120) REVERT: H 15 LEU cc_start: 0.8907 (mt) cc_final: 0.8539 (mt) REVERT: H 50 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8250 (mm-40) REVERT: I 446 TRP cc_start: 0.8205 (t-100) cc_final: 0.7635 (t-100) REVERT: I 610 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: K 61 MET cc_start: 0.6853 (pmm) cc_final: 0.6414 (mpp) REVERT: L 36 GLN cc_start: 0.8600 (mt0) cc_final: 0.8304 (mt0) REVERT: L 97 GLU cc_start: 0.7546 (mp0) cc_final: 0.7286 (mp0) REVERT: L 101 GLN cc_start: 0.8269 (mm110) cc_final: 0.7751 (mt0) REVERT: N 130 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7914 (tp30) REVERT: N 195 ILE cc_start: 0.8478 (tt) cc_final: 0.7774 (mp) REVERT: O 322 ASN cc_start: 0.8437 (t0) cc_final: 0.8112 (t0) REVERT: O 345 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6912 (mt-10) REVERT: P 226 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (mp) REVERT: P 274 MET cc_start: 0.8142 (tpp) cc_final: 0.7919 (tpt) REVERT: Q 241 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7278 (tpt-90) REVERT: U 185 MET cc_start: 0.8928 (mmt) cc_final: 0.8412 (mmm) REVERT: U 258 ASP cc_start: 0.8185 (m-30) cc_final: 0.7739 (t0) REVERT: U 299 MET cc_start: 0.8432 (mmp) cc_final: 0.7815 (mmm) REVERT: Y 102 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: Y 137 LEU cc_start: 0.8599 (tp) cc_final: 0.8205 (pp) REVERT: Y 138 LYS cc_start: 0.6743 (pttm) cc_final: 0.6096 (tmmt) REVERT: Z 42 TRP cc_start: 0.5157 (t-100) cc_final: 0.4838 (t-100) REVERT: Z 83 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7339 (t-90) outliers start: 80 outliers final: 52 residues processed: 346 average time/residue: 0.1431 time to fit residues: 76.8052 Evaluate side-chains 310 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 131 HIS Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 226 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 241 ARG Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 306 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 102 GLU Chi-restraints excluded: chain Y residue 170 GLN Chi-restraints excluded: chain Z residue 65 PHE Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 124 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 181 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 0.0270 chunk 183 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN ** N 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 217 ASN U 218 GLN U 315 ASN ** Y 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.126757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094401 restraints weight = 42089.741| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.49 r_work: 0.3267 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19125 Z= 0.122 Angle : 0.553 8.865 25878 Z= 0.283 Chirality : 0.039 0.197 3091 Planarity : 0.004 0.109 3251 Dihedral : 5.124 63.192 2635 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.21 % Rotamer: Outliers : 4.36 % Allowed : 23.25 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.48 % 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: 1.81 (0.18), residues: 2401 helix: 2.56 (0.14), residues: 1431 sheet: 0.03 (0.34), residues: 245 loop : -1.25 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 58 TYR 0.020 0.001 TYR I 591 PHE 0.015 0.001 PHE Q 325 TRP 0.020 0.001 TRP K 89 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19125) covalent geometry : angle 0.55304 / 0.28 (25878) hydrogen bonds : bond 0.03845 / 2.63 ( 1254) hydrogen bonds : angle 4.22477 / 3.02 ( 3783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 282 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7859 (mp-120) REVERT: H 15 LEU cc_start: 0.8920 (mt) cc_final: 0.8539 (mt) REVERT: H 50 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8239 (mm-40) REVERT: I 331 MET cc_start: 0.0605 (tmm) cc_final: 0.0392 (tmm) REVERT: I 446 TRP cc_start: 0.8179 (t-100) cc_final: 0.7612 (t-100) REVERT: I 610 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: K 61 MET cc_start: 0.7055 (pmm) cc_final: 0.6541 (mpp) REVERT: K 101 LYS cc_start: 0.8805 (tptt) cc_final: 0.8568 (pttp) REVERT: L 25 GLN cc_start: 0.8022 (mt0) cc_final: 0.7604 (mm-40) REVERT: L 52 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: L 101 GLN cc_start: 0.8245 (mm110) cc_final: 0.7665 (mt0) REVERT: N 100 LYS cc_start: 0.7144 (mttt) cc_final: 0.6634 (mmtm) REVERT: N 195 ILE cc_start: 0.8459 (tt) cc_final: 0.7740 (mp) REVERT: N 271 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: N 392 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: N 448 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: O 322 ASN cc_start: 0.8462 (t0) cc_final: 0.8153 (t0) REVERT: O 345 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6941 (mt-10) REVERT: P 274 MET cc_start: 0.8133 (tpp) cc_final: 0.7888 (tpt) REVERT: Q 241 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7488 (tpt-90) REVERT: Q 335 MET cc_start: 0.8459 (ptp) cc_final: 0.8106 (ptt) REVERT: U 185 MET cc_start: 0.8940 (mmt) cc_final: 0.8443 (mmm) REVERT: U 242 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8139 (tp30) REVERT: U 258 ASP cc_start: 0.8168 (m-30) cc_final: 0.7764 (t0) REVERT: U 299 MET cc_start: 0.8357 (mmp) cc_final: 0.7835 (mmm) REVERT: Y 102 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: Y 137 LEU cc_start: 0.8710 (tp) cc_final: 0.8369 (pp) REVERT: Y 138 LYS cc_start: 0.6638 (pttm) cc_final: 0.6028 (tmmt) REVERT: Z 42 TRP cc_start: 0.5136 (t-100) cc_final: 0.4861 (t-100) REVERT: Z 58 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6870 (mm-30) REVERT: Z 83 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7381 (t-90) outliers start: 85 outliers final: 52 residues processed: 352 average time/residue: 0.1379 time to fit residues: 75.1172 Evaluate side-chains 307 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 569 MET Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 241 ARG Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 306 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 102 GLU Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 65 PHE Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 91 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 237 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 240 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 166 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN I 455 ASN I 487 HIS K 77 ASN N 423 ASN N 435 ASN U 218 GLN U 315 ASN ** Y 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.125715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093137 restraints weight = 41931.199| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.64 r_work: 0.3238 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19125 Z= 0.134 Angle : 0.566 9.275 25878 Z= 0.288 Chirality : 0.039 0.193 3091 Planarity : 0.004 0.104 3251 Dihedral : 5.107 62.601 2631 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.00 % Favored : 95.79 % Rotamer: Outliers : 4.47 % Allowed : 24.33 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.48 % 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: 1.90 (0.18), residues: 2401 helix: 2.64 (0.14), residues: 1429 sheet: 0.01 (0.33), residues: 246 loop : -1.21 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 23 TYR 0.017 0.001 TYR Y 91 PHE 0.016 0.001 PHE Q 325 TRP 0.025 0.001 TRP N 39 HIS 0.005 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (19125) covalent geometry : angle 0.56551 / 0.29 (25878) hydrogen bonds : bond 0.03753 / 2.57 ( 1254) hydrogen bonds : angle 4.08385 / 2.90 ( 3783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 267 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7866 (mp-120) REVERT: H 15 LEU cc_start: 0.8925 (mt) cc_final: 0.8539 (mt) REVERT: H 50 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8217 (mm-40) REVERT: H 56 ARG cc_start: 0.8814 (ptm160) cc_final: 0.8504 (ptm160) REVERT: I 331 MET cc_start: 0.1183 (tmm) cc_final: 0.0951 (tmm) REVERT: I 446 TRP cc_start: 0.8240 (t-100) cc_final: 0.7671 (t-100) REVERT: I 510 MET cc_start: 0.9124 (mmm) cc_final: 0.8696 (mpp) REVERT: K 101 LYS cc_start: 0.8870 (tptt) cc_final: 0.8638 (pttt) REVERT: L 25 GLN cc_start: 0.8088 (mt0) cc_final: 0.7645 (mm-40) REVERT: L 52 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: L 101 GLN cc_start: 0.8266 (mm110) cc_final: 0.7742 (mt0) REVERT: N 392 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: N 443 MET cc_start: 0.8147 (tpt) cc_final: 0.7900 (ttt) REVERT: N 448 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: O 305 MET cc_start: 0.8659 (mmm) cc_final: 0.8306 (mmt) REVERT: O 322 ASN cc_start: 0.8493 (t0) cc_final: 0.8206 (t0) REVERT: P 274 MET cc_start: 0.8150 (tpp) cc_final: 0.7901 (tpt) REVERT: Q 335 MET cc_start: 0.8567 (ptp) cc_final: 0.8264 (ptp) REVERT: U 185 MET cc_start: 0.8947 (mmt) cc_final: 0.8446 (mmm) REVERT: U 218 GLN cc_start: 0.8488 (tp40) cc_final: 0.8178 (tt0) REVERT: U 240 GLN cc_start: 0.8919 (tt0) cc_final: 0.8710 (mt0) REVERT: U 242 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8210 (tp30) REVERT: U 258 ASP cc_start: 0.8215 (m-30) cc_final: 0.7781 (t0) REVERT: U 299 MET cc_start: 0.8404 (mmp) cc_final: 0.7983 (mmm) REVERT: Y 137 LEU cc_start: 0.8727 (tp) cc_final: 0.8402 (pp) REVERT: Y 138 LYS cc_start: 0.6646 (pttm) cc_final: 0.6033 (tmmt) REVERT: Z 42 TRP cc_start: 0.5169 (t-100) cc_final: 0.4942 (t-100) REVERT: Z 58 GLU cc_start: 0.7708 (mm-30) cc_final: 0.6851 (mm-30) REVERT: Z 63 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8177 (tp-100) REVERT: Z 83 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7522 (t-90) outliers start: 87 outliers final: 58 residues processed: 338 average time/residue: 0.1300 time to fit residues: 69.0653 Evaluate side-chains 309 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 296 ASP Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 297 ASP Chi-restraints excluded: chain U residue 306 LEU Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 65 PHE Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 91 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 38 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 177 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 ASN K 14 ASN K 77 ASN N 423 ASN U 315 ASN Y 155 GLN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Y 198 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.125485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.093082 restraints weight = 41818.608| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.85 r_work: 0.3228 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19125 Z= 0.127 Angle : 0.558 9.153 25878 Z= 0.285 Chirality : 0.039 0.196 3091 Planarity : 0.004 0.099 3251 Dihedral : 4.965 61.873 2628 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.70 % Rotamer: Outliers : 4.57 % Allowed : 24.74 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.95 (0.18), residues: 2401 helix: 2.69 (0.14), residues: 1429 sheet: 0.06 (0.33), residues: 252 loop : -1.24 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 23 TYR 0.017 0.001 TYR Y 91 PHE 0.033 0.001 PHE P 315 TRP 0.022 0.001 TRP K 89 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19125) covalent geometry : angle 0.55794 / 0.28 (25878) hydrogen bonds : bond 0.03698 / 2.53 ( 1254) hydrogen bonds : angle 4.00761 / 2.84 ( 3783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 270 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7801 (mp-120) REVERT: H 15 LEU cc_start: 0.8814 (mt) cc_final: 0.8435 (mt) REVERT: H 50 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8289 (mm-40) REVERT: H 56 ARG cc_start: 0.8850 (ptm160) cc_final: 0.8465 (ptm160) REVERT: I 331 MET cc_start: 0.1225 (tmm) cc_final: 0.0995 (tmm) REVERT: I 446 TRP cc_start: 0.8235 (t-100) cc_final: 0.7666 (t-100) REVERT: L 25 GLN cc_start: 0.7960 (mt0) cc_final: 0.7614 (mm-40) REVERT: L 52 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: L 101 GLN cc_start: 0.8235 (mm110) cc_final: 0.7778 (mt0) REVERT: N 25 MET cc_start: 0.7831 (mmm) cc_final: 0.7626 (tpt) REVERT: N 100 LYS cc_start: 0.7191 (mttt) cc_final: 0.6726 (mmtm) REVERT: N 392 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: N 448 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: O 305 MET cc_start: 0.8435 (mmm) cc_final: 0.8031 (mmt) REVERT: O 322 ASN cc_start: 0.8393 (t0) cc_final: 0.8150 (t0) REVERT: P 274 MET cc_start: 0.7800 (tpp) cc_final: 0.7540 (tpt) REVERT: Q 265 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: U 185 MET cc_start: 0.8929 (mmt) cc_final: 0.8419 (mmm) REVERT: U 242 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8063 (tp30) REVERT: U 258 ASP cc_start: 0.8018 (m-30) cc_final: 0.7656 (t0) REVERT: U 299 MET cc_start: 0.8407 (mmp) cc_final: 0.7934 (mmm) REVERT: Y 102 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8021 (tm-30) REVERT: Y 138 LYS cc_start: 0.6406 (pttm) cc_final: 0.5899 (tmmt) REVERT: Z 58 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6817 (mm-30) REVERT: Z 83 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7442 (t-90) outliers start: 89 outliers final: 61 residues processed: 342 average time/residue: 0.1243 time to fit residues: 66.4008 Evaluate side-chains 308 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 241 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 569 MET Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 392 GLU Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 241 ARG Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 297 ASP Chi-restraints excluded: chain U residue 315 ASN Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 91 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 82 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 0.0070 chunk 234 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN H 113 GLN ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN L 24 ASN N 423 ASN O 295 HIS O 339 ASN Q 337 ASN U 240 GLN U 315 ASN Y 77 GLN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Y 198 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.124104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091487 restraints weight = 41436.067| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.67 r_work: 0.3204 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19125 Z= 0.154 Angle : 0.577 9.213 25878 Z= 0.296 Chirality : 0.040 0.199 3091 Planarity : 0.004 0.098 3251 Dihedral : 4.853 61.828 2626 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.05 % Favored : 95.79 % Rotamer: Outliers : 4.88 % Allowed : 24.13 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.91 (0.18), residues: 2401 helix: 2.67 (0.14), residues: 1424 sheet: 0.03 (0.33), residues: 252 loop : -1.24 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 23 TYR 0.022 0.001 TYR U 171 PHE 0.022 0.002 PHE P 315 TRP 0.023 0.001 TRP K 89 HIS 0.004 0.001 HIS I 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (19125) covalent geometry : angle 0.57678 / 0.30 (25878) hydrogen bonds : bond 0.03763 / 2.57 ( 1254) hydrogen bonds : angle 3.99983 / 2.84 ( 3783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 252 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7788 (mp-120) REVERT: H 15 LEU cc_start: 0.8883 (mt) cc_final: 0.8510 (mt) REVERT: H 50 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8283 (mm-40) REVERT: I 331 MET cc_start: 0.1677 (tmm) cc_final: 0.1400 (tmm) REVERT: I 446 TRP cc_start: 0.8300 (t-100) cc_final: 0.7857 (t-100) REVERT: I 510 MET cc_start: 0.9050 (mmm) cc_final: 0.8652 (mpp) REVERT: L 52 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: L 101 GLN cc_start: 0.8341 (mm110) cc_final: 0.7990 (mt0) REVERT: N 448 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: O 322 ASN cc_start: 0.8523 (t0) cc_final: 0.8278 (t0) REVERT: P 274 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7938 (tpt) REVERT: Q 335 MET cc_start: 0.8536 (ptp) cc_final: 0.8241 (ptt) REVERT: U 185 MET cc_start: 0.8978 (mmt) cc_final: 0.8457 (mmm) REVERT: U 242 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8326 (tp30) REVERT: U 258 ASP cc_start: 0.8273 (m-30) cc_final: 0.7944 (t70) REVERT: U 299 MET cc_start: 0.8451 (mmp) cc_final: 0.8049 (mmm) REVERT: Y 102 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8172 (tm-30) REVERT: Y 123 MET cc_start: 0.7610 (mmm) cc_final: 0.7071 (mmt) REVERT: Y 138 LYS cc_start: 0.6599 (pttm) cc_final: 0.5878 (tmmt) REVERT: Z 58 GLU cc_start: 0.7877 (mm-30) cc_final: 0.6859 (mm-30) REVERT: Z 63 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8200 (tp-100) REVERT: Z 83 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7783 (t-90) outliers start: 95 outliers final: 69 residues processed: 330 average time/residue: 0.1137 time to fit residues: 59.1220 Evaluate side-chains 314 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 240 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 241 ARG Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 290 LEU Chi-restraints excluded: chain U residue 297 ASP Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 89 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN ** L 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 240 GLN Y 69 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Y 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.123894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091076 restraints weight = 41653.212| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.78 r_work: 0.3196 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19125 Z= 0.149 Angle : 0.577 9.775 25878 Z= 0.296 Chirality : 0.040 0.200 3091 Planarity : 0.004 0.096 3251 Dihedral : 4.810 61.251 2626 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 4.57 % Allowed : 24.95 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.91 (0.18), residues: 2401 helix: 2.66 (0.14), residues: 1424 sheet: 0.04 (0.33), residues: 251 loop : -1.23 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 74 TYR 0.016 0.001 TYR Y 91 PHE 0.020 0.002 PHE P 315 TRP 0.025 0.001 TRP K 89 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (19125) covalent geometry : angle 0.57721 / 0.30 (25878) hydrogen bonds : bond 0.03728 / 2.54 ( 1254) hydrogen bonds : angle 3.98019 / 2.83 ( 3783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 250 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7788 (mp-120) REVERT: H 15 LEU cc_start: 0.8894 (mt) cc_final: 0.8551 (mt) REVERT: H 50 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8298 (mm-40) REVERT: H 75 LYS cc_start: 0.5690 (OUTLIER) cc_final: 0.5482 (mtmt) REVERT: H 102 GLN cc_start: 0.8530 (pp30) cc_final: 0.8328 (pp30) REVERT: I 331 MET cc_start: 0.1405 (tmm) cc_final: 0.1121 (tmm) REVERT: I 446 TRP cc_start: 0.8420 (t-100) cc_final: 0.7847 (t-100) REVERT: L 8 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8757 (mp) REVERT: L 25 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7966 (mm-40) REVERT: L 52 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: L 101 GLN cc_start: 0.8369 (mm110) cc_final: 0.8059 (mt0) REVERT: N 448 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: O 321 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: O 322 ASN cc_start: 0.8567 (t0) cc_final: 0.8062 (t0) REVERT: P 274 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7842 (tpt) REVERT: Q 335 MET cc_start: 0.8562 (ptp) cc_final: 0.8272 (ptt) REVERT: U 185 MET cc_start: 0.9003 (mmt) cc_final: 0.8461 (mmm) REVERT: U 218 GLN cc_start: 0.8720 (tp40) cc_final: 0.8472 (tt0) REVERT: U 231 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9154 (ttpp) REVERT: U 242 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8351 (tp30) REVERT: U 258 ASP cc_start: 0.8257 (m-30) cc_final: 0.7957 (t70) REVERT: U 286 ASP cc_start: 0.7717 (t0) cc_final: 0.7425 (t0) REVERT: U 299 MET cc_start: 0.8468 (mmp) cc_final: 0.8051 (mmm) REVERT: Y 102 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8103 (tm-30) REVERT: Y 104 GLU cc_start: 0.7355 (tp30) cc_final: 0.6568 (pp20) REVERT: Y 123 MET cc_start: 0.7560 (mmm) cc_final: 0.7091 (mmt) REVERT: Y 138 LYS cc_start: 0.6570 (pttm) cc_final: 0.5871 (tmmt) REVERT: Z 58 GLU cc_start: 0.7938 (mm-30) cc_final: 0.6905 (mm-30) REVERT: Z 63 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8259 (tp-100) REVERT: Z 83 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7849 (t-90) outliers start: 89 outliers final: 67 residues processed: 324 average time/residue: 0.1332 time to fit residues: 67.4886 Evaluate side-chains 310 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 321 GLN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 241 ARG Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 231 LYS Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 297 ASP Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 6 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 chunk 236 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN H 102 GLN ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN ** L 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Y 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.123369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.090641 restraints weight = 41647.181| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.73 r_work: 0.3183 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19125 Z= 0.155 Angle : 0.589 9.489 25878 Z= 0.302 Chirality : 0.041 0.202 3091 Planarity : 0.004 0.096 3251 Dihedral : 4.824 60.355 2626 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 4.52 % Allowed : 25.72 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.91 (0.18), residues: 2401 helix: 2.68 (0.14), residues: 1420 sheet: 0.06 (0.33), residues: 251 loop : -1.24 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 74 TYR 0.015 0.001 TYR Y 91 PHE 0.018 0.002 PHE P 315 TRP 0.026 0.001 TRP K 89 HIS 0.005 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (19125) covalent geometry : angle 0.58921 / 0.30 (25878) hydrogen bonds : bond 0.03752 / 2.56 ( 1254) hydrogen bonds : angle 3.98728 / 2.83 ( 3783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 250 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7866 (mp-120) REVERT: H 15 LEU cc_start: 0.8898 (mt) cc_final: 0.8569 (mt) REVERT: I 331 MET cc_start: 0.1296 (tmm) cc_final: 0.0984 (tmm) REVERT: I 446 TRP cc_start: 0.8463 (t-100) cc_final: 0.7817 (t-100) REVERT: I 510 MET cc_start: 0.9028 (mmm) cc_final: 0.8664 (mpp) REVERT: K 58 ARG cc_start: 0.7791 (ptt90) cc_final: 0.7378 (ptt-90) REVERT: L 25 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8037 (mm-40) REVERT: L 52 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: N 37 LEU cc_start: 0.8668 (pp) cc_final: 0.8279 (mt) REVERT: N 100 LYS cc_start: 0.8007 (mttt) cc_final: 0.7438 (mmtm) REVERT: N 299 VAL cc_start: 0.9144 (t) cc_final: 0.8926 (p) REVERT: N 448 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: O 321 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: P 274 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7952 (tpt) REVERT: Q 335 MET cc_start: 0.8582 (ptp) cc_final: 0.8295 (ptt) REVERT: U 185 MET cc_start: 0.9050 (mmt) cc_final: 0.8521 (mmm) REVERT: U 218 GLN cc_start: 0.8764 (tp40) cc_final: 0.8543 (tt0) REVERT: U 231 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9133 (ttpp) REVERT: U 242 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8406 (tp30) REVERT: U 258 ASP cc_start: 0.8285 (m-30) cc_final: 0.8022 (t70) REVERT: U 299 MET cc_start: 0.8517 (mmp) cc_final: 0.8081 (mmm) REVERT: Y 79 GLN cc_start: 0.8295 (tp40) cc_final: 0.8061 (tp-100) REVERT: Y 102 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8191 (tm-30) REVERT: Y 104 GLU cc_start: 0.7273 (tp30) cc_final: 0.6531 (pp20) REVERT: Y 123 MET cc_start: 0.7602 (mmm) cc_final: 0.7199 (mmt) REVERT: Y 138 LYS cc_start: 0.6568 (pttm) cc_final: 0.5852 (tmmt) REVERT: Z 58 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7036 (mm-30) REVERT: Z 63 GLN cc_start: 0.8550 (tp-100) cc_final: 0.8325 (tp-100) REVERT: Z 83 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.7918 (t-90) outliers start: 88 outliers final: 68 residues processed: 321 average time/residue: 0.1253 time to fit residues: 62.3535 Evaluate side-chains 309 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 163 TYR Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 321 GLN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 217 ILE Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 241 ARG Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 231 LYS Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 297 ASP Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Z residue 17 THR Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 89 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 228 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN L 241 GLN O 295 HIS Y 69 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.123109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090296 restraints weight = 41458.860| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.71 r_work: 0.3183 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19125 Z= 0.154 Angle : 0.593 9.419 25878 Z= 0.305 Chirality : 0.041 0.199 3091 Planarity : 0.004 0.095 3251 Dihedral : 4.876 59.863 2626 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.34 % Favored : 95.50 % Rotamer: Outliers : 4.21 % Allowed : 26.13 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.90 (0.18), residues: 2401 helix: 2.67 (0.14), residues: 1416 sheet: 0.10 (0.33), residues: 251 loop : -1.26 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 74 TYR 0.016 0.001 TYR Y 91 PHE 0.017 0.002 PHE I 436 TRP 0.027 0.001 TRP K 89 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (19125) covalent geometry : angle 0.59259 / 0.31 (25878) hydrogen bonds : bond 0.03750 / 2.56 ( 1254) hydrogen bonds : angle 3.98489 / 2.83 ( 3783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 241 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 11 ARG cc_start: 0.8308 (tpt90) cc_final: 0.8094 (tpt90) REVERT: H 13 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7847 (mp-120) REVERT: H 15 LEU cc_start: 0.8874 (mt) cc_final: 0.8505 (mt) REVERT: H 50 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8124 (mm-40) REVERT: I 331 MET cc_start: 0.1428 (tmm) cc_final: 0.1081 (tmm) REVERT: I 446 TRP cc_start: 0.8471 (t-100) cc_final: 0.7789 (t-100) REVERT: I 510 MET cc_start: 0.9024 (mmm) cc_final: 0.8703 (mpp) REVERT: L 52 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: N 37 LEU cc_start: 0.8705 (pp) cc_final: 0.8348 (mt) REVERT: N 100 LYS cc_start: 0.8089 (mttt) cc_final: 0.7648 (mmtm) REVERT: N 448 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: O 321 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: P 274 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7881 (tpt) REVERT: Q 335 MET cc_start: 0.8578 (ptp) cc_final: 0.8298 (ptt) REVERT: U 185 MET cc_start: 0.9054 (mmt) cc_final: 0.8511 (mmm) REVERT: U 231 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9153 (ttpp) REVERT: U 242 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8393 (tp30) REVERT: U 258 ASP cc_start: 0.8288 (m-30) cc_final: 0.8035 (t70) REVERT: U 299 MET cc_start: 0.8526 (mmp) cc_final: 0.8095 (mmm) REVERT: Y 104 GLU cc_start: 0.7307 (tp30) cc_final: 0.6634 (pp20) REVERT: Y 123 MET cc_start: 0.7576 (mmm) cc_final: 0.7198 (mmt) REVERT: Y 138 LYS cc_start: 0.6634 (pttm) cc_final: 0.5880 (tmmt) REVERT: Z 58 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7068 (mm-30) REVERT: Z 83 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7920 (t-90) outliers start: 82 outliers final: 63 residues processed: 312 average time/residue: 0.1392 time to fit residues: 67.4347 Evaluate side-chains 303 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 519 LEU Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 163 TYR Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 321 GLN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 217 ILE Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 262 ILE Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 231 LYS Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 89 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 123 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 173 optimal weight: 0.0670 chunk 171 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 GLN ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN L 241 GLN U 288 ASN Y 69 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.124169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091348 restraints weight = 41586.032| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.74 r_work: 0.3204 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19125 Z= 0.129 Angle : 0.599 10.065 25878 Z= 0.307 Chirality : 0.040 0.196 3091 Planarity : 0.004 0.095 3251 Dihedral : 4.790 57.634 2625 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 3.34 % Allowed : 27.16 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.93 (0.18), residues: 2401 helix: 2.69 (0.14), residues: 1415 sheet: 0.12 (0.34), residues: 243 loop : -1.20 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 74 TYR 0.017 0.001 TYR Y 91 PHE 0.016 0.001 PHE P 315 TRP 0.028 0.001 TRP K 89 HIS 0.005 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19125) covalent geometry : angle 0.59937 / 0.31 (25878) hydrogen bonds : bond 0.03640 / 2.48 ( 1254) hydrogen bonds : angle 3.94332 / 2.80 ( 3783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 LEU cc_start: 0.8687 (mt) cc_final: 0.8374 (mt) REVERT: H 50 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8109 (mm-40) REVERT: I 331 MET cc_start: 0.1433 (tmm) cc_final: 0.1037 (tmm) REVERT: I 446 TRP cc_start: 0.8423 (t-100) cc_final: 0.7741 (t-100) REVERT: K 58 ARG cc_start: 0.7657 (ptt90) cc_final: 0.7197 (ptt-90) REVERT: L 52 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: N 37 LEU cc_start: 0.8693 (pp) cc_final: 0.8352 (mt) REVERT: N 100 LYS cc_start: 0.7972 (mttt) cc_final: 0.7418 (mmtm) REVERT: N 448 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: O 295 HIS cc_start: 0.7863 (m-70) cc_final: 0.7605 (m-70) REVERT: O 322 ASN cc_start: 0.8567 (t0) cc_final: 0.8082 (t0) REVERT: P 274 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7837 (tpt) REVERT: Q 335 MET cc_start: 0.8534 (ptp) cc_final: 0.8264 (ptt) REVERT: U 185 MET cc_start: 0.9066 (mmt) cc_final: 0.8535 (mmm) REVERT: U 213 LYS cc_start: 0.8989 (tmmt) cc_final: 0.8786 (tttp) REVERT: U 231 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9132 (ttpp) REVERT: U 242 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8399 (tp30) REVERT: U 258 ASP cc_start: 0.8265 (m-30) cc_final: 0.8024 (t70) REVERT: U 299 MET cc_start: 0.8444 (mmp) cc_final: 0.8030 (mmm) REVERT: Y 54 MET cc_start: 0.8225 (mmm) cc_final: 0.7946 (mmm) REVERT: Y 104 GLU cc_start: 0.7386 (tp30) cc_final: 0.6724 (pp20) REVERT: Y 123 MET cc_start: 0.7603 (mmm) cc_final: 0.7227 (mmt) REVERT: Y 138 LYS cc_start: 0.6589 (pttm) cc_final: 0.5865 (tmmt) REVERT: Z 58 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7130 (mm-30) REVERT: Z 83 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7916 (t-90) outliers start: 65 outliers final: 57 residues processed: 299 average time/residue: 0.1423 time to fit residues: 66.0246 Evaluate side-chains 300 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 530 TYR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 61 MET Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 139 GLN Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 209 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 438 PHE Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 448 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 200 GLU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 224 LEU Chi-restraints excluded: chain O residue 232 SER Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 269 THR Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 275 ASN Chi-restraints excluded: chain P residue 279 SER Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain P residue 322 SER Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 263 SER Chi-restraints excluded: chain Q residue 267 ASN Chi-restraints excluded: chain Q residue 329 SER Chi-restraints excluded: chain U residue 231 LYS Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 59 GLN Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Z residue 83 HIS Chi-restraints excluded: chain Z residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 167 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN L 241 GLN Y 69 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.123398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.090436 restraints weight = 41751.287| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.81 r_work: 0.3183 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19125 Z= 0.148 Angle : 0.605 9.612 25878 Z= 0.310 Chirality : 0.040 0.193 3091 Planarity : 0.004 0.093 3251 Dihedral : 4.769 59.800 2623 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 3.39 % Allowed : 26.95 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % 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: 1.93 (0.18), residues: 2401 helix: 2.68 (0.14), residues: 1415 sheet: 0.15 (0.33), residues: 251 loop : -1.22 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 11 TYR 0.016 0.001 TYR Y 91 PHE 0.018 0.002 PHE I 436 TRP 0.027 0.001 TRP K 89 HIS 0.005 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (19125) covalent geometry : angle 0.60479 / 0.31 (25878) hydrogen bonds : bond 0.03673 / 2.50 ( 1254) hydrogen bonds : angle 3.95092 / 2.81 ( 3783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6674.71 seconds wall clock time: 114 minutes 28.28 seconds (6868.28 seconds total)