Starting phenix.real_space_refine on Sun Apr 5 20:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5v_55596/04_2026/9t5v_55596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5v_55596/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9t5v_55596/04_2026/9t5v_55596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5v_55596/04_2026/9t5v_55596.map" model { file = "/net/cci-nas-00/data/ceres_data/9t5v_55596/04_2026/9t5v_55596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5v_55596/04_2026/9t5v_55596.cif" } 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-2.1rc1-6017/lib/python3.9/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, 32 Unusual residues: {' CA': 3, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 17 Unusual residues: {' CA': 2, ' MN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 2.80, 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: 1.14 Conformation dependent library (CDL) restraints added in 527.0 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: 0.59 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: 1.80 Time building geometry restraints manager: 1.46 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 2.320 nonbonded pdb=" OE1 GLU A 320 " pdb="MN MN B2001 " model vdw 2.103 2.320 nonbonded pdb="MN MN B2001 " pdb=" O HOH B2102 " model vdw 2.129 2.320 nonbonded pdb=" OE2 GLU B 212 " pdb="MN MN B2001 " model vdw 2.132 2.320 nonbonded pdb="MN MN A1203 " pdb=" O HOH A1302 " model vdw 2.143 2.320 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 covalent geometry : bond 0.01135 (13172) covalent geometry : angle 1.53900 (17831) SS BOND : bond 0.00438 ( 20) SS BOND : angle 1.41272 ( 40) hydrogen bonds : bond 0.13449 ( 472) hydrogen bonds : angle 7.63393 ( 1275) link_ALPHA1-3 : bond 0.01225 ( 2) link_ALPHA1-3 : angle 3.34323 ( 6) link_ALPHA1-6 : bond 0.00540 ( 2) link_ALPHA1-6 : angle 2.26755 ( 6) link_BETA1-4 : bond 0.02274 ( 8) link_BETA1-4 : angle 6.83948 ( 24) link_NAG-ASN : bond 0.07351 ( 8) link_NAG-ASN : angle 8.61307 ( 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 : 0.435 Fit side-chains revert: symmetry clash REVERT: A 137 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: A 174 MET cc_start: 0.3736 (OUTLIER) cc_final: 0.3194 (tpt) 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: -0.1564 (mtm) REVERT: C 212 MET cc_start: 0.0223 (mmt) cc_final: -0.0286 (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: 0.0885 time to fit residues: 12.0398 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 : 0.485 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 431 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.133508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075886 restraints weight = 33868.985| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.19 r_work: 0.3096 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13212 Z= 0.126 Angle : 0.684 13.057 17931 Z= 0.326 Chirality : 0.047 0.382 2026 Planarity : 0.005 0.059 2325 Dihedral : 11.381 107.392 2223 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 3.19 % Allowed : 21.59 % Favored : 75.22 % 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: -1.49 (0.20), residues: 1624 helix: -0.55 (0.26), residues: 359 sheet: -0.45 (0.25), residues: 419 loop : -1.44 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.017 0.001 TYR C 393 PHE 0.021 0.001 PHE A 121 TRP 0.014 0.001 TRP C 117 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00275 (13172) covalent geometry : angle 0.65746 (17831) SS BOND : bond 0.00180 ( 20) SS BOND : angle 0.95411 ( 40) hydrogen bonds : bond 0.03357 ( 472) hydrogen bonds : angle 5.81491 ( 1275) link_ALPHA1-3 : bond 0.00949 ( 2) link_ALPHA1-3 : angle 2.90107 ( 6) link_ALPHA1-6 : bond 0.00561 ( 2) link_ALPHA1-6 : angle 2.53248 ( 6) link_BETA1-4 : bond 0.00506 ( 8) link_BETA1-4 : angle 3.06602 ( 24) link_NAG-ASN : bond 0.00722 ( 8) link_NAG-ASN : angle 3.71238 ( 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 98 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 54 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.7981 (t0) REVERT: A 36 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: A 137 PHE cc_start: 0.7518 (m-80) cc_final: 0.6557 (m-80) REVERT: A 174 MET cc_start: 0.3601 (OUTLIER) cc_final: 0.3366 (tpp) REVERT: A 220 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7298 (tpm170) REVERT: A 227 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7000 (p0) REVERT: A 246 PHE cc_start: 0.7517 (t80) cc_final: 0.7304 (t80) REVERT: A 323 GLN cc_start: 0.7547 (mm110) cc_final: 0.6554 (pp30) REVERT: A 332 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7404 (t-90) REVERT: A 362 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 212 MET cc_start: -0.0141 (mmt) cc_final: -0.0415 (ptp) REVERT: C 421 MET cc_start: 0.7657 (ppp) cc_final: 0.7400 (ppp) outliers start: 44 outliers final: 17 residues processed: 94 average time/residue: 0.0967 time to fit residues: 14.0070 Evaluate side-chains 72 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 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 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 207 ASN 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: 0.9980 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 431 ASN A 600 GLN B 373 GLN B 400 GLN C 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.132640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074675 restraints weight = 34144.697| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.35 r_work: 0.3067 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13212 Z= 0.153 Angle : 0.635 11.504 17931 Z= 0.307 Chirality : 0.046 0.331 2026 Planarity : 0.004 0.054 2325 Dihedral : 8.819 100.142 2191 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.50 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 21.16 % Favored : 75.58 % 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: -1.06 (0.20), residues: 1624 helix: 0.17 (0.27), residues: 359 sheet: -0.36 (0.25), residues: 421 loop : -1.25 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 302 TYR 0.016 0.001 TYR C 393 PHE 0.022 0.001 PHE A 121 TRP 0.009 0.001 TRP B 23 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00343 (13172) covalent geometry : angle 0.60903 (17831) SS BOND : bond 0.00171 ( 20) SS BOND : angle 0.88269 ( 40) hydrogen bonds : bond 0.03088 ( 472) hydrogen bonds : angle 5.56539 ( 1275) link_ALPHA1-3 : bond 0.00892 ( 2) link_ALPHA1-3 : angle 2.89780 ( 6) link_ALPHA1-6 : bond 0.00711 ( 2) link_ALPHA1-6 : angle 2.61723 ( 6) link_BETA1-4 : bond 0.00343 ( 8) link_BETA1-4 : angle 2.97386 ( 24) link_NAG-ASN : bond 0.00713 ( 8) link_NAG-ASN : angle 3.37923 ( 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 95 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 50 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.3986 (OUTLIER) cc_final: 0.3760 (tpp) REVERT: A 220 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7430 (tpm170) REVERT: A 227 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7212 (p0) REVERT: A 323 GLN cc_start: 0.7557 (mm110) cc_final: 0.6602 (pp30) REVERT: A 332 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7593 (t-90) REVERT: A 362 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9009 (p) REVERT: C 218 ASN cc_start: 0.5622 (m-40) cc_final: 0.5279 (p0) REVERT: C 421 MET cc_start: 0.7735 (ppp) cc_final: 0.7405 (ppp) outliers start: 45 outliers final: 22 residues processed: 90 average time/residue: 0.0979 time to fit residues: 13.4815 Evaluate side-chains 73 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 220 ARG 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 362 VAL 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 511 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 716 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 420 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: 2.9990 chunk 75 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.132806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074946 restraints weight = 33969.793| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.28 r_work: 0.3070 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13212 Z= 0.128 Angle : 0.608 11.274 17931 Z= 0.295 Chirality : 0.045 0.331 2026 Planarity : 0.004 0.051 2325 Dihedral : 8.158 103.202 2186 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.44 % Rotamer: Outliers : 3.62 % Allowed : 20.72 % Favored : 75.65 % 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: -0.86 (0.21), residues: 1624 helix: 0.47 (0.27), residues: 365 sheet: -0.27 (0.25), residues: 421 loop : -1.18 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.014 0.001 TYR C 393 PHE 0.019 0.001 PHE A 121 TRP 0.010 0.001 TRP C 160 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00284 (13172) covalent geometry : angle 0.58372 (17831) SS BOND : bond 0.00167 ( 20) SS BOND : angle 0.83344 ( 40) hydrogen bonds : bond 0.02870 ( 472) hydrogen bonds : angle 5.40016 ( 1275) link_ALPHA1-3 : bond 0.01041 ( 2) link_ALPHA1-3 : angle 2.82350 ( 6) link_ALPHA1-6 : bond 0.01047 ( 2) link_ALPHA1-6 : angle 2.55284 ( 6) link_BETA1-4 : bond 0.00365 ( 8) link_BETA1-4 : angle 2.82231 ( 24) link_NAG-ASN : bond 0.00664 ( 8) link_NAG-ASN : angle 3.25312 ( 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 102 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 52 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8187 (t0) REVERT: A 220 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7529 (tpm170) REVERT: A 323 GLN cc_start: 0.7333 (mm110) cc_final: 0.6615 (pp30) REVERT: A 332 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7597 (t-90) REVERT: C 39 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (ttp80) REVERT: C 101 MET cc_start: -0.1373 (OUTLIER) cc_final: -0.1814 (mmm) REVERT: C 218 ASN cc_start: 0.5516 (m-40) cc_final: 0.5291 (p0) REVERT: C 421 MET cc_start: 0.7711 (ppp) cc_final: 0.7499 (ppp) outliers start: 50 outliers final: 28 residues processed: 96 average time/residue: 0.0931 time to fit residues: 14.0268 Evaluate side-chains 78 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 45 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 440 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 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 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 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: 3.9990 chunk 134 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** 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 = 0.4387 r_free = 0.4387 target = 0.132596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074388 restraints weight = 34133.838| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.31 r_work: 0.3061 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13212 Z= 0.146 Angle : 0.611 10.960 17931 Z= 0.298 Chirality : 0.045 0.352 2026 Planarity : 0.004 0.050 2325 Dihedral : 7.576 104.805 2181 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.41 % Allowed : 21.67 % Favored : 74.93 % 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: -0.69 (0.21), residues: 1624 helix: 0.70 (0.28), residues: 365 sheet: -0.19 (0.25), residues: 421 loop : -1.10 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.014 0.001 TYR C 393 PHE 0.022 0.001 PHE A 121 TRP 0.009 0.001 TRP C 160 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00328 (13172) covalent geometry : angle 0.58726 (17831) SS BOND : bond 0.00170 ( 20) SS BOND : angle 0.81031 ( 40) hydrogen bonds : bond 0.02851 ( 472) hydrogen bonds : angle 5.28901 ( 1275) link_ALPHA1-3 : bond 0.00911 ( 2) link_ALPHA1-3 : angle 2.71579 ( 6) link_ALPHA1-6 : bond 0.01107 ( 2) link_ALPHA1-6 : angle 2.34998 ( 6) link_BETA1-4 : bond 0.00423 ( 8) link_BETA1-4 : angle 2.75579 ( 24) link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 3.31339 ( 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 98 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 51 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7594 (tpm170) REVERT: A 332 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7707 (t-90) REVERT: B 414 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9237 (mm) REVERT: C 101 MET cc_start: -0.1223 (OUTLIER) cc_final: -0.1494 (mmm) REVERT: C 330 ASP cc_start: 0.4574 (OUTLIER) cc_final: 0.4226 (t0) outliers start: 47 outliers final: 34 residues processed: 91 average time/residue: 0.0982 time to fit residues: 14.1371 Evaluate side-chains 86 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 47 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 256 ILE 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 437 ILE 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 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 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 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 330 ASP 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: 7.9990 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** 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 = 0.4375 r_free = 0.4375 target = 0.131933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.073888 restraints weight = 33691.658| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.42 r_work: 0.3052 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13212 Z= 0.164 Angle : 0.622 10.943 17931 Z= 0.304 Chirality : 0.046 0.345 2026 Planarity : 0.004 0.049 2325 Dihedral : 7.153 105.542 2179 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.33 % Allowed : 21.96 % Favored : 74.71 % 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: 366 sheet: -0.14 (0.25), residues: 417 loop : -1.09 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.015 0.001 TYR C 393 PHE 0.022 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 covalent geometry : bond 0.00372 (13172) covalent geometry : angle 0.59896 (17831) SS BOND : bond 0.00199 ( 20) SS BOND : angle 1.12992 ( 40) hydrogen bonds : bond 0.02908 ( 472) hydrogen bonds : angle 5.32541 ( 1275) link_ALPHA1-3 : bond 0.00961 ( 2) link_ALPHA1-3 : angle 2.61556 ( 6) link_ALPHA1-6 : bond 0.01247 ( 2) link_ALPHA1-6 : angle 1.83028 ( 6) link_BETA1-4 : bond 0.00430 ( 8) link_BETA1-4 : angle 2.72740 ( 24) link_NAG-ASN : bond 0.00680 ( 8) link_NAG-ASN : angle 3.21563 ( 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 100 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 54 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8041 (t0) REVERT: A 137 PHE cc_start: 0.7686 (m-80) cc_final: 0.7170 (m-80) REVERT: A 174 MET cc_start: 0.4215 (tpt) cc_final: 0.3996 (mmm) REVERT: A 220 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7619 (tpm170) REVERT: A 246 PHE cc_start: 0.7375 (t80) cc_final: 0.7164 (t80) REVERT: A 332 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7648 (t-90) REVERT: B 243 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: B 414 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9257 (mm) REVERT: C 101 MET cc_start: -0.1122 (OUTLIER) cc_final: -0.1396 (mmm) REVERT: C 413 TRP cc_start: 0.9191 (t60) cc_final: 0.8884 (t60) outliers start: 46 outliers final: 34 residues processed: 96 average time/residue: 0.0975 time to fit residues: 14.8326 Evaluate side-chains 91 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 239 VAL Chi-restraints excluded: chain A residue 256 ILE 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 437 ILE 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 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 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 243 ASP 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 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: 2.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074454 restraints weight = 33842.385| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.28 r_work: 0.3065 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13212 Z= 0.123 Angle : 0.600 10.789 17931 Z= 0.294 Chirality : 0.045 0.342 2026 Planarity : 0.004 0.047 2325 Dihedral : 6.919 105.139 2179 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -0.54 (0.21), residues: 1624 helix: 0.89 (0.28), residues: 366 sheet: -0.08 (0.25), residues: 420 loop : -1.06 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.020 0.001 TYR C 422 PHE 0.020 0.001 PHE A 121 TRP 0.018 0.001 TRP C 117 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00274 (13172) covalent geometry : angle 0.57868 (17831) SS BOND : bond 0.00211 ( 20) SS BOND : angle 0.92235 ( 40) hydrogen bonds : bond 0.02753 ( 472) hydrogen bonds : angle 5.22736 ( 1275) link_ALPHA1-3 : bond 0.01078 ( 2) link_ALPHA1-3 : angle 2.44889 ( 6) link_ALPHA1-6 : bond 0.01264 ( 2) link_ALPHA1-6 : angle 1.56144 ( 6) link_BETA1-4 : bond 0.00427 ( 8) link_BETA1-4 : angle 2.63667 ( 24) link_NAG-ASN : bond 0.00617 ( 8) link_NAG-ASN : angle 3.09301 ( 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 95 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 54 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.7917 (t0) REVERT: A 137 PHE cc_start: 0.7657 (m-80) cc_final: 0.7177 (m-80) REVERT: A 174 MET cc_start: 0.4086 (tpt) cc_final: 0.3849 (mmm) REVERT: A 220 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7617 (tpm170) REVERT: A 246 PHE cc_start: 0.7202 (t80) cc_final: 0.6994 (t80) REVERT: A 332 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7643 (t-90) REVERT: B 414 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9220 (mm) REVERT: C 39 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8085 (ttp80) REVERT: C 101 MET cc_start: -0.1204 (OUTLIER) cc_final: -0.1465 (mmm) REVERT: C 413 TRP cc_start: 0.9208 (t60) cc_final: 0.8911 (t60) outliers start: 41 outliers final: 29 residues processed: 90 average time/residue: 0.0950 time to fit residues: 13.5282 Evaluate side-chains 87 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 239 VAL Chi-restraints excluded: chain A residue 256 ILE 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 659 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 665 LEU 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 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 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: 7.9990 chunk 18 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 127 optimal weight: 0.0060 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** 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 = 0.4379 r_free = 0.4379 target = 0.132696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074425 restraints weight = 33972.680| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.37 r_work: 0.3047 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13212 Z= 0.123 Angle : 0.590 10.620 17931 Z= 0.289 Chirality : 0.045 0.341 2026 Planarity : 0.004 0.047 2325 Dihedral : 6.793 104.659 2179 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.04 % Allowed : 22.75 % 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: -0.50 (0.21), residues: 1624 helix: 0.96 (0.28), residues: 366 sheet: -0.05 (0.25), residues: 426 loop : -1.05 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.015 0.001 TYR C 393 PHE 0.018 0.001 PHE A 121 TRP 0.014 0.001 TRP C 117 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00273 (13172) covalent geometry : angle 0.56896 (17831) SS BOND : bond 0.00209 ( 20) SS BOND : angle 0.95295 ( 40) hydrogen bonds : bond 0.02698 ( 472) hydrogen bonds : angle 5.10458 ( 1275) link_ALPHA1-3 : bond 0.01117 ( 2) link_ALPHA1-3 : angle 2.33593 ( 6) link_ALPHA1-6 : bond 0.01173 ( 2) link_ALPHA1-6 : angle 1.44817 ( 6) link_BETA1-4 : bond 0.00431 ( 8) link_BETA1-4 : angle 2.59761 ( 24) link_NAG-ASN : bond 0.00610 ( 8) link_NAG-ASN : angle 3.00836 ( 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 97 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8067 (t0) REVERT: A 137 PHE cc_start: 0.7670 (m-80) cc_final: 0.7203 (m-80) REVERT: A 220 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7650 (tpm170) REVERT: A 323 GLN cc_start: 0.8095 (mp10) cc_final: 0.6929 (pp30) REVERT: A 332 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7715 (t-90) REVERT: B 414 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9260 (mm) REVERT: C 101 MET cc_start: -0.1200 (OUTLIER) cc_final: -0.1443 (mmm) REVERT: C 413 TRP cc_start: 0.9232 (t60) cc_final: 0.8906 (t60) outliers start: 42 outliers final: 30 residues processed: 92 average time/residue: 0.1067 time to fit residues: 14.8410 Evaluate side-chains 87 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 239 VAL Chi-restraints excluded: chain A residue 256 ILE 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 437 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 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 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 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 101 MET 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: 2.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 3 optimal weight: 0.0770 chunk 136 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4362 r_free = 0.4362 target = 0.132132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073482 restraints weight = 34271.765| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.42 r_work: 0.3023 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2240 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= 0.144 Angle : 0.621 13.183 17931 Z= 0.303 Chirality : 0.046 0.339 2026 Planarity : 0.004 0.047 2325 Dihedral : 6.810 104.464 2179 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.83 % Allowed : 22.97 % 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: -0.46 (0.21), residues: 1624 helix: 1.00 (0.28), residues: 366 sheet: -0.04 (0.25), residues: 421 loop : -1.02 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 39 TYR 0.013 0.001 TYR C 393 PHE 0.019 0.001 PHE A 121 TRP 0.012 0.001 TRP C 117 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00324 (13172) covalent geometry : angle 0.60161 (17831) SS BOND : bond 0.00166 ( 20) SS BOND : angle 0.80588 ( 40) hydrogen bonds : bond 0.02763 ( 472) hydrogen bonds : angle 5.13022 ( 1275) link_ALPHA1-3 : bond 0.01023 ( 2) link_ALPHA1-3 : angle 2.31864 ( 6) link_ALPHA1-6 : bond 0.01187 ( 2) link_ALPHA1-6 : angle 1.49585 ( 6) link_BETA1-4 : bond 0.00395 ( 8) link_BETA1-4 : angle 2.59607 ( 24) link_NAG-ASN : bond 0.00622 ( 8) link_NAG-ASN : angle 3.01098 ( 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 91 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 52 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8015 (t0) REVERT: A 137 PHE cc_start: 0.7638 (m-80) cc_final: 0.7191 (m-80) REVERT: A 174 MET cc_start: 0.4304 (tpt) cc_final: 0.4028 (tpt) REVERT: A 220 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7770 (tpm170) REVERT: A 332 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7775 (t70) REVERT: B 414 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9216 (mm) REVERT: C 413 TRP cc_start: 0.9244 (t60) cc_final: 0.8901 (t60) outliers start: 39 outliers final: 32 residues processed: 86 average time/residue: 0.0853 time to fit residues: 11.8797 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 : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 171 PHE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 ILE 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 437 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 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 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 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 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 154 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN A 429 ASN A 431 ASN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.132092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073414 restraints weight = 34296.601| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.40 r_work: 0.3015 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13212 Z= 0.142 Angle : 0.616 10.944 17931 Z= 0.300 Chirality : 0.045 0.338 2026 Planarity : 0.004 0.046 2325 Dihedral : 6.735 104.507 2179 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.75 % Allowed : 23.04 % 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: -0.43 (0.21), residues: 1624 helix: 1.02 (0.28), residues: 366 sheet: -0.01 (0.25), residues: 427 loop : -1.01 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 39 TYR 0.014 0.001 TYR C 393 PHE 0.020 0.001 PHE A 121 TRP 0.013 0.001 TRP C 117 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00322 (13172) covalent geometry : angle 0.59719 (17831) SS BOND : bond 0.00178 ( 20) SS BOND : angle 0.87904 ( 40) hydrogen bonds : bond 0.02749 ( 472) hydrogen bonds : angle 5.07420 ( 1275) link_ALPHA1-3 : bond 0.01167 ( 2) link_ALPHA1-3 : angle 2.35308 ( 6) link_ALPHA1-6 : bond 0.01108 ( 2) link_ALPHA1-6 : angle 1.52333 ( 6) link_BETA1-4 : bond 0.00395 ( 8) link_BETA1-4 : angle 2.54892 ( 24) link_NAG-ASN : bond 0.00632 ( 8) link_NAG-ASN : angle 2.96624 ( 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 89 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 51 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 137 PHE cc_start: 0.7511 (m-80) cc_final: 0.7103 (m-80) REVERT: A 238 VAL cc_start: 0.6629 (OUTLIER) cc_final: 0.6410 (p) REVERT: A 323 GLN cc_start: 0.8195 (mp10) cc_final: 0.6966 (pp30) REVERT: A 332 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7789 (t-90) REVERT: B 414 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9203 (mm) REVERT: C 98 MET cc_start: 0.0061 (tpp) cc_final: -0.1205 (mtp) REVERT: C 413 TRP cc_start: 0.9201 (t60) cc_final: 0.8873 (t60) outliers start: 38 outliers final: 32 residues processed: 86 average time/residue: 0.1039 time to fit residues: 13.9092 Evaluate side-chains 84 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 48 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 ILE 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 437 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 511 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 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 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 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: 20.0000 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.132016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073382 restraints weight = 34021.372| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.50 r_work: 0.3013 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 13212 Z= 0.228 Angle : 0.853 59.192 17931 Z= 0.482 Chirality : 0.047 0.510 2026 Planarity : 0.004 0.046 2325 Dihedral : 6.742 104.824 2179 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.90 % Allowed : 22.83 % Favored : 74.28 % Cbeta Deviations : 0.07 % 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: -0.44 (0.21), residues: 1624 helix: 1.03 (0.28), residues: 366 sheet: -0.06 (0.25), residues: 429 loop : -1.00 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 220 TYR 0.013 0.001 TYR C 393 PHE 0.020 0.001 PHE A 121 TRP 0.011 0.001 TRP C 117 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00432 (13172) covalent geometry : angle 0.84116 (17831) SS BOND : bond 0.00168 ( 20) SS BOND : angle 0.84562 ( 40) hydrogen bonds : bond 0.02746 ( 472) hydrogen bonds : angle 5.08720 ( 1275) link_ALPHA1-3 : bond 0.01034 ( 2) link_ALPHA1-3 : angle 2.39823 ( 6) link_ALPHA1-6 : bond 0.01001 ( 2) link_ALPHA1-6 : angle 1.52621 ( 6) link_BETA1-4 : bond 0.00425 ( 8) link_BETA1-4 : angle 2.55863 ( 24) link_NAG-ASN : bond 0.00628 ( 8) link_NAG-ASN : angle 2.96518 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5781.20 seconds wall clock time: 98 minutes 43.48 seconds (5923.48 seconds total)