Starting phenix.real_space_refine on Fri Jul 3 09:27:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5v_55596/07_2026/9t5v_55596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5v_55596/07_2026/9t5v_55596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t5v_55596/07_2026/9t5v_55596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5v_55596/07_2026/9t5v_55596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t5v_55596/07_2026/9t5v_55596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5v_55596/07_2026/9t5v_55596.map" } resolution = 3.06 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= 0.029 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 2 7.51 5 S 69 5.16 5 C 8097 2.51 5 N 2237 2.21 5 O 2527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12937 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5803 Classifications: {'peptide': 751} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 715} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3573 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 434} Chain: "C" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3286 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 28 Ad-hoc single atom residues: {' CA': 3, ' MN': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' MN': 1, ' CA': 2} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.82, per 1000 atoms: 0.22 Number of scatterers: 12937 At special positions: 0 Unit cell: (84.11, 155.28, 218.686, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 Ca 5 19.99 S 69 16.00 O 2527 8.00 N 2237 7.00 C 8097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 409 " distance=2.03 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 241 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1205 " - " ASN A 677 " " NAG A1206 " - " ASN A 681 " " NAG B2004 " - " ASN B 232 " " NAG D 1 " - " ASN A 719 " " NAG E 1 " - " ASN A 70 " " NAG F 1 " - " ASN A 375 " " NAG G 1 " - " ASN B 190 " " NAG H 1 " - " ASN B 94 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 566.3 milliseconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 19 sheets defined 27.7% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.542A pdb=" N LYS A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.764A pdb=" N ASN A 227 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 228 " --> pdb=" O ILE A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 228' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.958A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 558 through 562 removed outlier: 3.598A pdb=" N SER A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 558 through 562' Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.788A pdb=" N GLY B 18 " --> pdb=" O CYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.656A pdb=" N CYS B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 114 through 119 removed outlier: 4.278A pdb=" N ASP B 119 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.579A pdb=" N GLY B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.830A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.867A pdb=" N SER B 274 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN B 275 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 277 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 304 through 313 removed outlier: 3.598A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 removed outlier: 3.545A pdb=" N VAL B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.748A pdb=" N GLY B 439 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.631A pdb=" N ILE B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 removed outlier: 3.908A pdb=" N HIS C 85 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 114 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.304A pdb=" N PHE C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 removed outlier: 3.567A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.835A pdb=" N LEU C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.561A pdb=" N LEU C 216 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 237 Processing helix chain 'C' and resid 247 through 263 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.926A pdb=" N ALA C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 308 through 326 Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.730A pdb=" N VAL C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 368 removed outlier: 3.864A pdb=" N THR C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C 356 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.736A pdb=" N MET A 9 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP A 585 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 575 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.499A pdb=" N GLN A 36 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 44 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 5.116A pdb=" N LEU A 87 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE A 110 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N CYS A 89 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE A 108 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A 106 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 184 removed outlier: 5.647A pdb=" N ILE A 182 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN A 175 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 184 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP A 134 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 238 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA A 136 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 240 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 138 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 235 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 267 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 237 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE A 269 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 239 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 397 removed outlier: 3.857A pdb=" N ALA A 391 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 397 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 430 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG A 420 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER A 428 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A 422 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.412A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 492 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 513 removed outlier: 6.276A pdb=" N LEU A 509 " --> pdb=" O GLY A 526 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A 526 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL A 511 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 524 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 513 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 554 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 543 removed outlier: 4.132A pdb=" N GLY A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 630 through 631 removed outlier: 3.713A pdb=" N LYS A 631 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 703 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 630 through 631 removed outlier: 3.713A pdb=" N LYS A 631 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 703 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 690 Processing sheet with id=AB4, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.580A pdb=" N LEU B 420 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 85 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 removed outlier: 5.977A pdb=" N TYR B 360 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 189 removed outlier: 5.171A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 188 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 105 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY B 145 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 107 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY B 147 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR B 109 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE B 149 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET B 111 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG B 235 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 297 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 237 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 299 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 239 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY B 321 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE B 298 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 8 Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.600A pdb=" N GLY C 11 " --> pdb=" O THR C 433 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG C 39 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLY C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 143 through 144 removed outlier: 3.940A pdb=" N ALA C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1275 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: 1.93 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2181 1.26 - 1.40: 3163 1.40 - 1.55: 7585 1.55 - 1.69: 146 1.69 - 1.83: 97 Bond restraints: 13172 Sorted by residual: bond pdb=" CG LEU A 170 " pdb=" CD2 LEU A 170 " ideal model delta sigma weight residual 1.521 1.174 0.347 3.30e-02 9.18e+02 1.11e+02 bond pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.413 1.566 -0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" CE1 TYR C 136 " pdb=" CZ TYR C 136 " ideal model delta sigma weight residual 1.378 1.558 -0.180 2.40e-02 1.74e+03 5.64e+01 bond pdb=" CE2 TYR C 136 " pdb=" CZ TYR C 136 " ideal model delta sigma weight residual 1.378 1.199 0.179 2.40e-02 1.74e+03 5.54e+01 bond pdb=" CE1 PHE C 331 " pdb=" CZ PHE C 331 " ideal model delta sigma weight residual 1.382 1.202 0.180 3.00e-02 1.11e+03 3.62e+01 ... (remaining 13167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.45: 17715 7.45 - 14.89: 103 14.89 - 22.34: 12 22.34 - 29.79: 0 29.79 - 37.23: 1 Bond angle restraints: 17831 Sorted by residual: angle pdb=" CA ILE B 414 " pdb=" CB ILE B 414 " pdb=" CG1 ILE B 414 " ideal model delta sigma weight residual 110.40 147.63 -37.23 1.70e+00 3.46e-01 4.80e+02 angle pdb=" OD1 ASN A 677 " pdb=" CG ASN A 677 " pdb=" ND2 ASN A 677 " ideal model delta sigma weight residual 122.60 113.03 9.57 1.00e+00 1.00e+00 9.16e+01 angle pdb=" OE1 GLU A 155 " pdb=" CD GLU A 155 " pdb=" OE2 GLU A 155 " ideal model delta sigma weight residual 122.90 100.88 22.02 2.40e+00 1.74e-01 8.42e+01 angle pdb=" CB ASN A 677 " pdb=" CG ASN A 677 " pdb=" ND2 ASN A 677 " ideal model delta sigma weight residual 116.40 103.60 12.80 1.50e+00 4.44e-01 7.29e+01 angle pdb=" C ARG A 152 " pdb=" N MET A 153 " pdb=" CA MET A 153 " ideal model delta sigma weight residual 121.58 107.97 13.61 1.95e+00 2.63e-01 4.87e+01 ... (remaining 17826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 7425 24.33 - 48.67: 636 48.67 - 73.00: 117 73.00 - 97.34: 33 97.34 - 121.67: 21 Dihedral angle restraints: 8232 sinusoidal: 3573 harmonic: 4659 Sorted by residual: dihedral pdb=" CA SER A 82 " pdb=" C SER A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual -180.00 -116.36 -63.64 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 176 " pdb=" CB CYS B 176 " ideal model delta sinusoidal sigma weight residual 93.00 157.46 -64.46 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 150.55 -57.55 1 1.00e+01 1.00e-02 4.45e+01 ... (remaining 8229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 2009 0.368 - 0.735: 12 0.735 - 1.103: 2 1.103 - 1.470: 1 1.470 - 1.838: 2 Chirality restraints: 2026 Sorted by residual: chirality pdb=" CB ILE B 414 " pdb=" CA ILE B 414 " pdb=" CG1 ILE B 414 " pdb=" CG2 ILE B 414 " both_signs ideal model delta sigma weight residual False 2.64 0.81 1.84 2.00e-01 2.50e+01 8.44e+01 chirality pdb=" C1 NAG A1205 " pdb=" ND2 ASN A 677 " pdb=" C2 NAG A1205 " pdb=" O5 NAG A1205 " both_signs ideal model delta sigma weight residual False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" C2 BMA E 3 " pdb=" C1 BMA E 3 " pdb=" C3 BMA E 3 " pdb=" O2 BMA E 3 " both_signs ideal model delta sigma weight residual False 2.47 1.15 1.33 2.00e-01 2.50e+01 4.39e+01 ... (remaining 2023 not shown) Planarity restraints: 2333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 677 " -0.078 2.00e-02 2.50e+03 1.78e-01 3.94e+02 pdb=" CG ASN A 677 " 0.201 2.00e-02 2.50e+03 pdb=" OD1 ASN A 677 " -0.184 2.00e-02 2.50e+03 pdb=" ND2 ASN A 677 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A1205 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 331 " -0.018 2.00e-02 2.50e+03 1.24e-01 2.68e+02 pdb=" CG PHE C 331 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE C 331 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 PHE C 331 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE C 331 " 0.219 2.00e-02 2.50e+03 pdb=" CE2 PHE C 331 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE C 331 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 190 " -0.144 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" CG ASN B 190 " 0.229 2.00e-02 2.50e+03 pdb=" OD1 ASN B 190 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 190 " 0.042 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.098 2.00e-02 2.50e+03 ... (remaining 2330 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 99 2.64 - 3.21: 11312 3.21 - 3.77: 20846 3.77 - 4.34: 27850 4.34 - 4.90: 45248 Nonbonded interactions: 105355 Sorted by model distance: nonbonded pdb="MN MN B2001 " pdb=" O HOH B2101 " model vdw 2.075 3.060 nonbonded pdb=" OE1 GLU A 320 " pdb="MN MN B2001 " model vdw 2.103 3.060 nonbonded pdb="MN MN B2001 " pdb=" O HOH B2102 " model vdw 2.129 3.060 nonbonded pdb=" OE2 GLU B 212 " pdb="MN MN B2001 " model vdw 2.132 3.060 nonbonded pdb="MN MN A1203 " pdb=" O HOH A1302 " model vdw 2.143 3.060 ... (remaining 105350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.011 0.347 13212 Z= 0.511 Angle : 1.590 37.233 17931 Z= 0.790 Chirality : 0.107 1.838 2026 Planarity : 0.015 0.306 2325 Dihedral : 19.451 121.672 5190 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 2.39 % Allowed : 23.41 % Favored : 74.20 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % 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: -2.47 (0.19), residues: 1624 helix: -2.24 (0.21), residues: 362 sheet: -0.65 (0.24), residues: 427 loop : -1.87 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.002 ARG B 375 TYR 0.124 0.012 TYR C 33 PHE 0.219 0.009 PHE C 331 TRP 0.089 0.007 TRP C 426 HIS 0.048 0.004 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.01135 / 0.50 (13172) covalent geometry : angle 1.53900 / 0.78 (17831) SS BOND : bond 0.00438 / 0.23 ( 20) SS BOND : angle 1.41272 / 0.92 ( 40) hydrogen bonds : bond 0.13449 / 9.08 ( 472) hydrogen bonds : angle 7.63393 / 5.28 ( 1275) link_ALPHA1-3 : bond 0.01225 / 0.60 ( 2) link_ALPHA1-3 : angle 3.34323 / 2.19 ( 6) link_ALPHA1-6 : bond 0.00540 / 0.28 ( 2) link_ALPHA1-6 : angle 2.26755 / 1.43 ( 6) link_BETA1-4 : bond 0.02274 / 1.09 ( 8) link_BETA1-4 : angle 6.83948 / 4.32 ( 24) link_NAG-ASN : bond 0.07351 / 3.73 ( 8) link_NAG-ASN : angle 8.61307 / 5.36 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6615 (m-80) REVERT: A 174 MET cc_start: 0.3736 (OUTLIER) cc_final: 0.3528 (mmm) REVERT: A 210 HIS cc_start: 0.5019 (OUTLIER) cc_final: 0.3235 (m-70) REVERT: A 718 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 270 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8681 (tp) REVERT: C 98 MET cc_start: -0.1028 (tpp) cc_final: -0.1540 (mtm) REVERT: C 212 MET cc_start: 0.0223 (mmt) cc_final: -0.0243 (ptp) REVERT: C 224 MET cc_start: -0.1623 (OUTLIER) cc_final: -0.2123 (pp-130) REVERT: C 357 MET cc_start: 0.3864 (mmp) cc_final: 0.3549 (tpt) outliers start: 33 outliers final: 19 residues processed: 84 average time/residue: 0.0775 time to fit residues: 10.5576 Evaluate side-chains 77 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 224 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN A 431 ASN B 207 ASN B 390 GLN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.133423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076006 restraints weight = 33862.472| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.21 r_work: 0.3100 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13212 Z= 0.130 Angle : 0.697 12.603 17931 Z= 0.334 Chirality : 0.048 0.390 2026 Planarity : 0.005 0.059 2325 Dihedral : 11.718 108.315 2223 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 3.19 % Allowed : 21.30 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.55 (0.20), residues: 1624 helix: -0.60 (0.26), residues: 359 sheet: -0.46 (0.25), residues: 419 loop : -1.50 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.017 0.001 TYR C 393 PHE 0.022 0.001 PHE A 121 TRP 0.011 0.001 TRP C 117 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (13172) covalent geometry : angle 0.67062 / 0.33 (17831) SS BOND : bond 0.00182 / 0.08 ( 20) SS BOND : angle 0.97375 / 0.61 ( 40) hydrogen bonds : bond 0.03455 / 2.29 ( 472) hydrogen bonds : angle 5.86953 / 4.04 ( 1275) link_ALPHA1-3 : bond 0.00884 / 0.43 ( 2) link_ALPHA1-3 : angle 2.83813 / 2.04 ( 6) link_ALPHA1-6 : bond 0.00573 / 0.29 ( 2) link_ALPHA1-6 : angle 2.42910 / 1.86 ( 6) link_BETA1-4 : bond 0.00554 / 0.27 ( 8) link_BETA1-4 : angle 3.20126 / 2.37 ( 24) link_NAG-ASN : bond 0.00997 / 0.51 ( 8) link_NAG-ASN : angle 3.64767 / 2.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 53 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7975 (t0) REVERT: A 36 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: A 137 PHE cc_start: 0.7481 (m-80) cc_final: 0.6923 (m-80) REVERT: A 174 MET cc_start: 0.3642 (OUTLIER) cc_final: 0.3391 (tpp) REVERT: A 220 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7259 (tpm170) REVERT: A 246 PHE cc_start: 0.7576 (t80) cc_final: 0.7369 (t80) REVERT: A 323 GLN cc_start: 0.7439 (mm110) cc_final: 0.6425 (pp30) REVERT: A 332 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7476 (t-90) REVERT: A 362 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8845 (p) REVERT: C 212 MET cc_start: -0.0153 (mmt) cc_final: -0.0436 (ptp) REVERT: C 421 MET cc_start: 0.7642 (ppp) cc_final: 0.7358 (ppp) outliers start: 44 outliers final: 19 residues processed: 92 average time/residue: 0.0936 time to fit residues: 13.4442 Evaluate side-chains 73 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 133 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 148 optimal weight: 30.0000 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 431 ASN A 600 GLN B 373 GLN B 400 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.131859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.075174 restraints weight = 34302.031| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.88 r_work: 0.3010 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13212 Z= 0.203 Angle : 0.664 11.437 17931 Z= 0.324 Chirality : 0.047 0.330 2026 Planarity : 0.004 0.056 2325 Dihedral : 8.870 99.295 2189 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 3.55 % Allowed : 21.01 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.15 (0.20), residues: 1624 helix: 0.12 (0.27), residues: 359 sheet: -0.41 (0.25), residues: 421 loop : -1.33 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.015 0.001 TYR C 393 PHE 0.024 0.001 PHE A 121 TRP 0.009 0.001 TRP B 23 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (13172) covalent geometry : angle 0.63853 / 0.32 (17831) SS BOND : bond 0.00169 / 0.08 ( 20) SS BOND : angle 0.91314 / 0.58 ( 40) hydrogen bonds : bond 0.03226 / 2.15 ( 472) hydrogen bonds : angle 5.64471 / 3.89 ( 1275) link_ALPHA1-3 : bond 0.00753 / 0.36 ( 2) link_ALPHA1-3 : angle 2.93302 / 1.97 ( 6) link_ALPHA1-6 : bond 0.00569 / 0.28 ( 2) link_ALPHA1-6 : angle 2.69469 / 1.81 ( 6) link_BETA1-4 : bond 0.00311 / 0.15 ( 8) link_BETA1-4 : angle 3.02661 / 2.17 ( 24) link_NAG-ASN : bond 0.00743 / 0.37 ( 8) link_NAG-ASN : angle 3.48775 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 49 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (ttt-90) REVERT: A 174 MET cc_start: 0.3985 (OUTLIER) cc_final: 0.3766 (tpp) REVERT: A 227 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7250 (p0) REVERT: A 323 GLN cc_start: 0.7465 (mm110) cc_final: 0.6581 (pp30) REVERT: A 332 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7607 (t-90) REVERT: C 101 MET cc_start: -0.2011 (mmt) cc_final: -0.2276 (mmm) REVERT: C 218 ASN cc_start: 0.5644 (m-40) cc_final: 0.5403 (p0) REVERT: C 421 MET cc_start: 0.7733 (ppp) cc_final: 0.7444 (ppp) outliers start: 49 outliers final: 24 residues processed: 94 average time/residue: 0.0938 time to fit residues: 13.6749 Evaluate side-chains 75 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.130752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071884 restraints weight = 34083.392| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.33 r_work: 0.3005 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13212 Z= 0.261 Angle : 0.683 11.452 17931 Z= 0.333 Chirality : 0.047 0.326 2026 Planarity : 0.004 0.055 2325 Dihedral : 8.399 104.560 2184 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 3.77 % Allowed : 20.87 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1624 helix: 0.48 (0.28), residues: 358 sheet: -0.37 (0.25), residues: 419 loop : -1.29 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 208 TYR 0.015 0.002 TYR A 390 PHE 0.028 0.002 PHE A 121 TRP 0.009 0.002 TRP C 160 HIS 0.007 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (13172) covalent geometry : angle 0.65728 / 0.33 (17831) SS BOND : bond 0.00194 / 0.09 ( 20) SS BOND : angle 0.92028 / 0.58 ( 40) hydrogen bonds : bond 0.03218 / 2.14 ( 472) hydrogen bonds : angle 5.57348 / 3.83 ( 1275) link_ALPHA1-3 : bond 0.00683 / 0.33 ( 2) link_ALPHA1-3 : angle 3.04163 / 1.98 ( 6) link_ALPHA1-6 : bond 0.00675 / 0.32 ( 2) link_ALPHA1-6 : angle 2.76759 / 1.98 ( 6) link_BETA1-4 : bond 0.00378 / 0.17 ( 8) link_BETA1-4 : angle 2.95441 / 2.14 ( 24) link_NAG-ASN : bond 0.00838 / 0.43 ( 8) link_NAG-ASN : angle 3.64589 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 55 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7654 (m-80) cc_final: 0.7260 (m-80) REVERT: A 163 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 220 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7248 (tpm170) REVERT: A 332 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7589 (t-90) REVERT: A 680 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (mptt) REVERT: B 414 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9198 (mm) REVERT: C 101 MET cc_start: -0.1062 (OUTLIER) cc_final: -0.1493 (mmm) outliers start: 52 outliers final: 31 residues processed: 100 average time/residue: 0.0867 time to fit residues: 13.4258 Evaluate side-chains 86 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 50 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 30 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.131321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.073529 restraints weight = 34285.948| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.22 r_work: 0.3042 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13212 Z= 0.152 Angle : 0.635 11.199 17931 Z= 0.309 Chirality : 0.046 0.334 2026 Planarity : 0.004 0.051 2325 Dihedral : 7.863 106.195 2181 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.55 % Allowed : 21.38 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1624 helix: 0.55 (0.28), residues: 364 sheet: -0.30 (0.25), residues: 414 loop : -1.21 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 208 TYR 0.013 0.001 TYR C 393 PHE 0.024 0.001 PHE A 121 TRP 0.008 0.001 TRP C 338 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (13172) covalent geometry : angle 0.61103 / 0.30 (17831) SS BOND : bond 0.00177 / 0.08 ( 20) SS BOND : angle 0.84134 / 0.52 ( 40) hydrogen bonds : bond 0.02994 / 1.97 ( 472) hydrogen bonds : angle 5.43300 / 3.73 ( 1275) link_ALPHA1-3 : bond 0.01114 / 0.53 ( 2) link_ALPHA1-3 : angle 2.91773 / 1.94 ( 6) link_ALPHA1-6 : bond 0.00993 / 0.48 ( 2) link_ALPHA1-6 : angle 2.50362 / 1.84 ( 6) link_BETA1-4 : bond 0.00458 / 0.21 ( 8) link_BETA1-4 : angle 2.75959 / 2.00 ( 24) link_NAG-ASN : bond 0.00668 / 0.33 ( 8) link_NAG-ASN : angle 3.34022 / 1.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 51 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8574 (ttt-90) REVERT: A 137 PHE cc_start: 0.7701 (m-80) cc_final: 0.7282 (m-80) REVERT: A 163 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 220 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7256 (tpm170) REVERT: A 332 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7626 (t-90) REVERT: A 680 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8309 (mptt) REVERT: B 414 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9223 (mm) REVERT: C 101 MET cc_start: -0.1220 (OUTLIER) cc_final: -0.1688 (mmm) outliers start: 49 outliers final: 30 residues processed: 93 average time/residue: 0.0905 time to fit residues: 12.9508 Evaluate side-chains 86 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 50 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 40.0000 chunk 144 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.131078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073286 restraints weight = 33870.937| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.21 r_work: 0.3040 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13212 Z= 0.171 Angle : 0.633 10.932 17931 Z= 0.308 Chirality : 0.046 0.336 2026 Planarity : 0.004 0.051 2325 Dihedral : 7.511 106.392 2179 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.41 % Allowed : 21.09 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1624 helix: 0.67 (0.28), residues: 364 sheet: -0.22 (0.25), residues: 421 loop : -1.14 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.016 0.001 TYR C 422 PHE 0.023 0.001 PHE A 121 TRP 0.008 0.001 TRP C 338 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13172) covalent geometry : angle 0.61059 / 0.30 (17831) SS BOND : bond 0.00163 / 0.08 ( 20) SS BOND : angle 0.83828 / 0.52 ( 40) hydrogen bonds : bond 0.02953 / 1.94 ( 472) hydrogen bonds : angle 5.35900 / 3.68 ( 1275) link_ALPHA1-3 : bond 0.00878 / 0.42 ( 2) link_ALPHA1-3 : angle 2.68958 / 1.78 ( 6) link_ALPHA1-6 : bond 0.01139 / 0.54 ( 2) link_ALPHA1-6 : angle 2.18894 / 1.62 ( 6) link_BETA1-4 : bond 0.00417 / 0.19 ( 8) link_BETA1-4 : angle 2.74203 / 1.99 ( 24) link_NAG-ASN : bond 0.00679 / 0.34 ( 8) link_NAG-ASN : angle 3.29153 / 1.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 54 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7772 (m-80) cc_final: 0.7366 (m-80) REVERT: A 163 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 174 MET cc_start: 0.4278 (tpt) cc_final: 0.4022 (mmm) REVERT: A 220 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7244 (tpm170) REVERT: A 323 GLN cc_start: 0.7528 (mm110) cc_final: 0.6642 (pp30) REVERT: A 332 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7724 (t-90) REVERT: A 591 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8735 (tt0) REVERT: A 680 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8278 (mptt) REVERT: B 414 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9249 (mm) REVERT: C 101 MET cc_start: -0.1125 (mmt) cc_final: -0.1576 (mmm) outliers start: 47 outliers final: 35 residues processed: 97 average time/residue: 0.0935 time to fit residues: 14.0862 Evaluate side-chains 92 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 52 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 56 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 126 optimal weight: 40.0000 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.131889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074471 restraints weight = 34135.211| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.27 r_work: 0.3076 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13212 Z= 0.120 Angle : 0.615 10.739 17931 Z= 0.301 Chirality : 0.046 0.339 2026 Planarity : 0.004 0.048 2325 Dihedral : 7.269 105.586 2179 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.33 % Allowed : 21.88 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1624 helix: 0.73 (0.28), residues: 365 sheet: -0.15 (0.25), residues: 410 loop : -1.13 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.018 0.001 TYR C 422 PHE 0.029 0.001 PHE A 246 TRP 0.009 0.001 TRP C 338 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13172) covalent geometry : angle 0.59310 / 0.30 (17831) SS BOND : bond 0.00309 / 0.13 ( 20) SS BOND : angle 1.22223 / 0.96 ( 40) hydrogen bonds : bond 0.02863 / 1.87 ( 472) hydrogen bonds : angle 5.32578 / 3.67 ( 1275) link_ALPHA1-3 : bond 0.01170 / 0.56 ( 2) link_ALPHA1-3 : angle 2.50786 / 1.69 ( 6) link_ALPHA1-6 : bond 0.01171 / 0.56 ( 2) link_ALPHA1-6 : angle 1.74977 / 1.30 ( 6) link_BETA1-4 : bond 0.00444 / 0.20 ( 8) link_BETA1-4 : angle 2.63563 / 1.92 ( 24) link_NAG-ASN : bond 0.00615 / 0.31 ( 8) link_NAG-ASN : angle 3.11980 / 1.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 56 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7810 (m-80) cc_final: 0.7286 (m-80) REVERT: A 163 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 174 MET cc_start: 0.4226 (tpt) cc_final: 0.3948 (mmm) REVERT: A 220 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7245 (tpm170) REVERT: A 323 GLN cc_start: 0.7533 (mm110) cc_final: 0.6703 (pp30) REVERT: A 332 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7686 (t-90) REVERT: A 431 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8939 (p0) REVERT: A 680 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8287 (mptt) REVERT: B 414 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9289 (mm) outliers start: 46 outliers final: 30 residues processed: 98 average time/residue: 0.0826 time to fit residues: 12.4897 Evaluate side-chains 86 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 51 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.130640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071448 restraints weight = 34131.665| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.50 r_work: 0.2971 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13212 Z= 0.238 Angle : 0.669 10.782 17931 Z= 0.328 Chirality : 0.047 0.335 2026 Planarity : 0.004 0.050 2325 Dihedral : 7.352 105.442 2179 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.55 % Allowed : 22.10 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1624 helix: 0.76 (0.28), residues: 365 sheet: -0.21 (0.25), residues: 426 loop : -1.14 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.013 0.001 TYR C 393 PHE 0.022 0.001 PHE A 121 TRP 0.018 0.002 TRP C 117 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (13172) covalent geometry : angle 0.64814 / 0.32 (17831) SS BOND : bond 0.00176 / 0.09 ( 20) SS BOND : angle 0.93163 / 0.64 ( 40) hydrogen bonds : bond 0.03012 / 1.98 ( 472) hydrogen bonds : angle 5.35695 / 3.69 ( 1275) link_ALPHA1-3 : bond 0.00633 / 0.30 ( 2) link_ALPHA1-3 : angle 2.49071 / 1.60 ( 6) link_ALPHA1-6 : bond 0.01119 / 0.53 ( 2) link_ALPHA1-6 : angle 1.71446 / 1.22 ( 6) link_BETA1-4 : bond 0.00383 / 0.17 ( 8) link_BETA1-4 : angle 2.79355 / 1.99 ( 24) link_NAG-ASN : bond 0.00771 / 0.39 ( 8) link_NAG-ASN : angle 3.33426 / 1.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 52 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7688 (m-80) cc_final: 0.7271 (m-80) REVERT: A 163 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 174 MET cc_start: 0.4057 (tpt) cc_final: 0.3796 (mmm) REVERT: A 220 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7433 (tpm170) REVERT: A 238 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6553 (p) REVERT: A 332 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7771 (t-90) REVERT: A 431 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.9089 (p0) REVERT: A 591 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8634 (tt0) REVERT: A 650 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9056 (mt) REVERT: A 680 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8423 (mptt) REVERT: B 414 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9129 (mm) REVERT: C 101 MET cc_start: -0.1159 (mmt) cc_final: -0.1405 (mmm) outliers start: 49 outliers final: 32 residues processed: 95 average time/residue: 0.0859 time to fit residues: 12.8370 Evaluate side-chains 90 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 50 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.131767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074814 restraints weight = 34142.976| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.89 r_work: 0.2988 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13212 Z= 0.132 Angle : 0.632 11.613 17931 Z= 0.308 Chirality : 0.046 0.339 2026 Planarity : 0.004 0.048 2325 Dihedral : 7.173 105.143 2179 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.75 % Allowed : 22.97 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1624 helix: 0.80 (0.28), residues: 365 sheet: -0.17 (0.25), residues: 428 loop : -1.11 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.013 0.001 TYR C 393 PHE 0.022 0.001 PHE A 121 TRP 0.016 0.001 TRP C 117 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13172) covalent geometry : angle 0.60955 / 0.30 (17831) SS BOND : bond 0.00177 / 0.08 ( 20) SS BOND : angle 1.54791 / 1.25 ( 40) hydrogen bonds : bond 0.02819 / 1.84 ( 472) hydrogen bonds : angle 5.28429 / 3.64 ( 1275) link_ALPHA1-3 : bond 0.00997 / 0.48 ( 2) link_ALPHA1-3 : angle 2.35143 / 1.58 ( 6) link_ALPHA1-6 : bond 0.01145 / 0.55 ( 2) link_ALPHA1-6 : angle 1.49834 / 1.14 ( 6) link_BETA1-4 : bond 0.00407 / 0.19 ( 8) link_BETA1-4 : angle 2.62033 / 1.89 ( 24) link_NAG-ASN : bond 0.00618 / 0.31 ( 8) link_NAG-ASN : angle 3.11554 / 1.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 51 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7665 (m-80) cc_final: 0.7257 (m-80) REVERT: A 163 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 220 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7493 (tpm170) REVERT: A 238 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6734 (p) REVERT: A 323 GLN cc_start: 0.8290 (mp10) cc_final: 0.7112 (pp30) REVERT: A 332 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7777 (t-90) REVERT: A 431 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8908 (p0) REVERT: A 650 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9016 (mt) REVERT: A 680 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8430 (mptt) REVERT: B 414 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9188 (mm) REVERT: C 39 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8213 (ttp80) REVERT: C 101 MET cc_start: -0.0326 (mmt) cc_final: -0.0569 (mmm) outliers start: 38 outliers final: 28 residues processed: 86 average time/residue: 0.0820 time to fit residues: 11.0637 Evaluate side-chains 87 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 51 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074253 restraints weight = 34317.245| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.89 r_work: 0.2978 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13212 Z= 0.155 Angle : 0.634 10.473 17931 Z= 0.308 Chirality : 0.046 0.339 2026 Planarity : 0.004 0.049 2325 Dihedral : 7.098 105.101 2179 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.97 % Allowed : 22.75 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1624 helix: 0.83 (0.28), residues: 365 sheet: -0.17 (0.25), residues: 428 loop : -1.09 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.013 0.001 TYR C 393 PHE 0.023 0.001 PHE A 121 TRP 0.015 0.001 TRP C 117 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (13172) covalent geometry : angle 0.61172 / 0.30 (17831) SS BOND : bond 0.00182 / 0.08 ( 20) SS BOND : angle 1.40445 / 1.12 ( 40) hydrogen bonds : bond 0.02830 / 1.86 ( 472) hydrogen bonds : angle 5.25763 / 3.63 ( 1275) link_ALPHA1-3 : bond 0.01086 / 0.52 ( 2) link_ALPHA1-3 : angle 2.42239 / 1.61 ( 6) link_ALPHA1-6 : bond 0.01119 / 0.54 ( 2) link_ALPHA1-6 : angle 1.47964 / 1.14 ( 6) link_BETA1-4 : bond 0.00396 / 0.18 ( 8) link_BETA1-4 : angle 2.63265 / 1.89 ( 24) link_NAG-ASN : bond 0.00638 / 0.32 ( 8) link_NAG-ASN : angle 3.10986 / 1.79 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 51 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7662 (m-80) cc_final: 0.7233 (m-80) REVERT: A 163 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 220 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7523 (tpm170) REVERT: A 238 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7171 (p) REVERT: A 268 VAL cc_start: 0.8254 (p) cc_final: 0.8029 (m) REVERT: A 323 GLN cc_start: 0.8230 (mp10) cc_final: 0.6975 (pp30) REVERT: A 332 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (t-90) REVERT: A 431 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8865 (p0) REVERT: A 591 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: A 650 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9034 (mt) REVERT: A 680 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8457 (mptt) REVERT: B 414 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9178 (mm) REVERT: C 39 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8201 (ttp80) REVERT: C 98 MET cc_start: 0.0106 (tpp) cc_final: -0.1163 (mtp) outliers start: 41 outliers final: 32 residues processed: 88 average time/residue: 0.0838 time to fit residues: 11.6178 Evaluate side-chains 91 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 50 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.130837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073871 restraints weight = 34085.729| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.87 r_work: 0.2971 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13212 Z= 0.176 Angle : 0.636 10.425 17931 Z= 0.311 Chirality : 0.046 0.340 2026 Planarity : 0.004 0.048 2325 Dihedral : 7.063 104.821 2179 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.19 % Allowed : 22.61 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1624 helix: 0.84 (0.28), residues: 365 sheet: -0.15 (0.25), residues: 426 loop : -1.10 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.013 0.001 TYR C 393 PHE 0.024 0.001 PHE A 121 TRP 0.017 0.001 TRP C 189 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (13172) covalent geometry : angle 0.61401 / 0.31 (17831) SS BOND : bond 0.00175 / 0.08 ( 20) SS BOND : angle 1.33243 / 1.05 ( 40) hydrogen bonds : bond 0.02859 / 1.88 ( 472) hydrogen bonds : angle 5.26211 / 3.63 ( 1275) link_ALPHA1-3 : bond 0.00998 / 0.48 ( 2) link_ALPHA1-3 : angle 2.40798 / 1.59 ( 6) link_ALPHA1-6 : bond 0.01024 / 0.49 ( 2) link_ALPHA1-6 : angle 1.47857 / 1.14 ( 6) link_BETA1-4 : bond 0.00396 / 0.18 ( 8) link_BETA1-4 : angle 2.64446 / 1.88 ( 24) link_NAG-ASN : bond 0.00675 / 0.34 ( 8) link_NAG-ASN : angle 3.13099 / 1.81 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.38 seconds wall clock time: 79 minutes 6.48 seconds (4746.48 seconds total)