Starting phenix.real_space_refine on Sun Aug 24 20:18:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg2_33805/08_2025/7yg2_33805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg2_33805/08_2025/7yg2_33805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yg2_33805/08_2025/7yg2_33805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg2_33805/08_2025/7yg2_33805.map" model { file = "/net/cci-nas-00/data/ceres_data/7yg2_33805/08_2025/7yg2_33805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg2_33805/08_2025/7yg2_33805.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2196 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 13078 2.51 5 N 3521 2.21 5 O 4079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 23 Chain: "M" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2257 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "I" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.76, per 1000 atoms: 0.23 Number of scatterers: 20783 At special positions: 0 Unit cell: (87.74, 175.48, 194.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4079 8.00 N 3521 7.00 C 13078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS M 162 " - pdb=" SG CYS M 334 " distance=2.03 Simple disulfide: pdb=" SG CYS M 168 " - pdb=" SG CYS M 323 " distance=2.03 Simple disulfide: pdb=" SG CYS M 358 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 372 " - pdb=" SG CYS M 393 " distance=2.03 Simple disulfide: pdb=" SG CYS M 441 " - pdb=" SG CYS M 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.04 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 701.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5058 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 53 sheets defined 19.2% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'M' and resid 164 through 171 removed outlier: 3.531A pdb=" N CYS M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 210 Processing helix chain 'M' and resid 216 through 223 Processing helix chain 'M' and resid 228 through 249 Processing helix chain 'M' and resid 252 through 272 Processing helix chain 'M' and resid 279 through 297 removed outlier: 3.635A pdb=" N LYS M 283 " --> pdb=" O THR M 279 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE M 286 " --> pdb=" O SER M 282 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THR M 287 " --> pdb=" O LYS M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 313 Processing helix chain 'M' and resid 313 through 330 removed outlier: 3.504A pdb=" N VAL M 317 " --> pdb=" O ASN M 313 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA M 328 " --> pdb=" O GLY M 324 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN M 329 " --> pdb=" O TYR M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 373 removed outlier: 3.525A pdb=" N PHE M 373 " --> pdb=" O LYS M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 421 removed outlier: 3.556A pdb=" N THR M 409 " --> pdb=" O ASN M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 440 Processing helix chain 'M' and resid 451 through 456 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.646A pdb=" N GLY A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.729A pdb=" N GLU B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.757A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 524 through 531 removed outlier: 4.041A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.779A pdb=" N LEU C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.530A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 415 through 421 Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.519A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'E' and resid 553 through 558 removed outlier: 3.912A pdb=" N LYS E 558 " --> pdb=" O LYS E 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 460 through 466 Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.642A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'G' and resid 553 through 558 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.886A pdb=" N GLY H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 466 Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.542A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 467 Processing helix chain 'K' and resid 525 through 531 removed outlier: 3.886A pdb=" N GLY K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 Processing helix chain 'L' and resid 414 through 420 removed outlier: 3.901A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 467 removed outlier: 3.737A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 530 Processing helix chain 'J' and resid 64 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.575A pdb=" N ARG A 346 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 350 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.507A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 413 " --> pdb=" O THR A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.679A pdb=" N TRP A 382 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 381 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 427 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 425 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.835A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 519 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 501 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.835A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 519 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 476 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.834A pdb=" N GLN A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 535 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 7.261A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 566 through 568 Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 348 removed outlier: 4.051A pdb=" N LEU B 368 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 382 through 383 removed outlier: 3.737A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 456 removed outlier: 3.530A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 453 through 456 removed outlier: 3.530A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB5, first strand: chain 'C' and resid 379 through 384 removed outlier: 4.144A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 429 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 381 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.834A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.834A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB9, first strand: chain 'C' and resid 565 through 567 removed outlier: 3.629A pdb=" N VAL D 567 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 424 through 428 removed outlier: 3.812A pdb=" N VAL D 428 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU D 437 " --> pdb=" O VAL D 428 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 455 through 457 removed outlier: 3.677A pdb=" N LEU D 475 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 501 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 455 through 457 removed outlier: 3.677A pdb=" N LEU D 475 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AC5, first strand: chain 'D' and resid 535 through 539 removed outlier: 3.525A pdb=" N VAL D 538 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR D 548 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 424 through 427 Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.991A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.991A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD1, first strand: chain 'F' and resid 363 through 365 removed outlier: 4.319A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA F 411 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 389 through 391 removed outlier: 7.175A pdb=" N TRP F 382 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER F 381 " --> pdb=" O THR F 427 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR F 427 " --> pdb=" O SER F 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.655A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.655A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.196A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL G 567 " --> pdb=" O LEU H 566 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU K 566 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER H 565 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER K 565 " --> pdb=" O LEU L 566 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N MET L 568 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL K 567 " --> pdb=" O MET L 568 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL J 41 " --> pdb=" O VAL L 567 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU J 34 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 349 Processing sheet with id=AD8, first strand: chain 'G' and resid 379 through 383 removed outlier: 3.534A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER G 381 " --> pdb=" O THR G 427 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR G 427 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR G 425 " --> pdb=" O THR G 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 455 through 457 removed outlier: 4.896A pdb=" N THR G 471 " --> pdb=" O VAL G 523 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 523 " --> pdb=" O THR G 471 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR G 473 " --> pdb=" O LEU G 521 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU G 521 " --> pdb=" O THR G 473 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU G 475 " --> pdb=" O SER G 519 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER G 519 " --> pdb=" O LEU G 475 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR G 477 " --> pdb=" O ALA G 517 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 517 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE G 479 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 501 " --> pdb=" O ILE G 520 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 455 through 457 removed outlier: 4.896A pdb=" N THR G 471 " --> pdb=" O VAL G 523 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL G 523 " --> pdb=" O THR G 471 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR G 473 " --> pdb=" O LEU G 521 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU G 521 " --> pdb=" O THR G 473 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU G 475 " --> pdb=" O SER G 519 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER G 519 " --> pdb=" O LEU G 475 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR G 477 " --> pdb=" O ALA G 517 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA G 517 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE G 479 " --> pdb=" O TYR G 515 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE3, first strand: chain 'H' and resid 346 through 349 removed outlier: 4.036A pdb=" N LEU H 368 " --> pdb=" O PHE H 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.364A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL H 428 " --> pdb=" O LEU H 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU H 437 " --> pdb=" O VAL H 428 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.935A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.935A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE8, first strand: chain 'K' and resid 348 through 350 removed outlier: 3.755A pdb=" N ILE K 350 " --> pdb=" O THR K 366 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.589A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.516A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.516A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.915A pdb=" N MET K 489 " --> pdb=" O THR K 535 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR K 535 " --> pdb=" O MET K 489 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 381 through 383 removed outlier: 4.012A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.979A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 520 " --> pdb=" O VAL L 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL L 501 " --> pdb=" O ILE L 520 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.979A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET L 506 " --> pdb=" O PHE L 516 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 485 through 489 removed outlier: 3.832A pdb=" N PHE L 485 " --> pdb=" O ALA L 539 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR L 534 " --> pdb=" O VAL L 552 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL L 538 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR L 548 " --> pdb=" O VAL L 538 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 110 through 116 removed outlier: 3.887A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR J 126 " --> pdb=" O ALA J 111 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6747 1.34 - 1.46: 4867 1.46 - 1.58: 9534 1.58 - 1.70: 1 1.70 - 1.82: 142 Bond restraints: 21291 Sorted by residual: bond pdb=" C1 NAG G 601 " pdb=" O5 NAG G 601 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" C1 NAG H 601 " pdb=" O5 NAG H 601 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" CB PRO D 497 " pdb=" CG PRO D 497 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.45e+00 ... (remaining 21286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 28337 1.68 - 3.37: 637 3.37 - 5.05: 80 5.05 - 6.74: 30 6.74 - 8.42: 5 Bond angle restraints: 29089 Sorted by residual: angle pdb=" CA PRO D 497 " pdb=" N PRO D 497 " pdb=" CD PRO D 497 " ideal model delta sigma weight residual 112.00 105.15 6.85 1.40e+00 5.10e-01 2.40e+01 angle pdb=" N GLY A 531 " pdb=" CA GLY A 531 " pdb=" C GLY A 531 " ideal model delta sigma weight residual 111.36 116.91 -5.55 1.17e+00 7.31e-01 2.25e+01 angle pdb=" CA PRO E 497 " pdb=" N PRO E 497 " pdb=" CD PRO E 497 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C THR E 370 " pdb=" N ASP E 371 " pdb=" CA ASP E 371 " ideal model delta sigma weight residual 122.46 127.95 -5.49 1.41e+00 5.03e-01 1.51e+01 angle pdb=" C THR A 530 " pdb=" N GLY A 531 " pdb=" CA GLY A 531 " ideal model delta sigma weight residual 119.92 123.57 -3.65 9.60e-01 1.09e+00 1.45e+01 ... (remaining 29084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 12208 23.03 - 46.06: 798 46.06 - 69.08: 56 69.08 - 92.11: 34 92.11 - 115.14: 21 Dihedral angle restraints: 13117 sinusoidal: 5369 harmonic: 7748 Sorted by residual: dihedral pdb=" CB CYS D 367 " pdb=" SG CYS D 367 " pdb=" SG CYS D 426 " pdb=" CB CYS D 426 " ideal model delta sinusoidal sigma weight residual 93.00 162.63 -69.63 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS L 575 " pdb=" SG CYS L 575 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS F 367 " pdb=" SG CYS F 367 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual 93.00 34.82 58.18 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 13114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3092 0.085 - 0.170: 318 0.170 - 0.256: 4 0.256 - 0.341: 0 0.341 - 0.426: 1 Chirality restraints: 3415 Sorted by residual: chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL H 390 " pdb=" CA VAL H 390 " pdb=" CG1 VAL H 390 " pdb=" CG2 VAL H 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1 NAG G 601 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG G 601 " pdb=" O5 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3412 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 496 " 0.093 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO E 497 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO E 497 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO E 497 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 496 " -0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO D 497 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 497 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 497 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 457 " -0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 458 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " -0.050 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1199 2.74 - 3.28: 20363 3.28 - 3.82: 33211 3.82 - 4.36: 38461 4.36 - 4.90: 66350 Nonbonded interactions: 159584 Sorted by model distance: nonbonded pdb=" O MET L 489 " pdb=" OG1 THR L 535 " model vdw 2.196 3.040 nonbonded pdb=" O ALA H 448 " pdb=" OG SER H 480 " model vdw 2.228 3.040 nonbonded pdb=" O ILE B 350 " pdb=" OG1 THR B 366 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASN L 563 " pdb=" ND2 ASN J 36 " model vdw 2.295 3.120 nonbonded pdb=" OG1 THR B 383 " pdb=" OG1 THR B 425 " model vdw 2.295 3.040 ... (remaining 159579 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 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.440 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21330 Z= 0.138 Angle : 0.625 14.350 29179 Z= 0.319 Chirality : 0.046 0.426 3415 Planarity : 0.006 0.138 3712 Dihedral : 15.078 115.141 7978 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2592 helix: -0.34 (0.23), residues: 470 sheet: 0.28 (0.20), residues: 687 loop : -0.48 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 491 TYR 0.023 0.001 TYR B 500 PHE 0.029 0.002 PHE C 348 TRP 0.037 0.001 TRP D 418 HIS 0.009 0.001 HIS K 430 Details of bonding type rmsd covalent geometry : bond 0.00292 (21291) covalent geometry : angle 0.60835 (29089) SS BOND : bond 0.00216 ( 27) SS BOND : angle 0.85500 ( 54) hydrogen bonds : bond 0.23920 ( 598) hydrogen bonds : angle 9.24349 ( 1842) link_BETA1-4 : bond 0.01421 ( 1) link_BETA1-4 : angle 1.14811 ( 3) link_NAG-ASN : bond 0.00725 ( 11) link_NAG-ASN : angle 4.18640 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 270 ILE cc_start: 0.7017 (mt) cc_final: 0.6814 (mt) REVERT: M 332 ASN cc_start: 0.6987 (t0) cc_final: 0.6766 (t0) REVERT: M 340 ILE cc_start: 0.7267 (tp) cc_final: 0.7051 (tp) REVERT: A 402 ASN cc_start: 0.3916 (p0) cc_final: 0.3569 (m110) REVERT: A 570 ASP cc_start: 0.7458 (t70) cc_final: 0.7201 (t0) REVERT: C 364 LYS cc_start: 0.7365 (pttp) cc_final: 0.6767 (mttt) REVERT: E 419 ASN cc_start: 0.8601 (m110) cc_final: 0.8339 (m110) REVERT: G 529 ASN cc_start: 0.6988 (m-40) cc_final: 0.6314 (m-40) REVERT: H 529 ASN cc_start: 0.7269 (m-40) cc_final: 0.7051 (m-40) REVERT: K 416 ASP cc_start: 0.8084 (p0) cc_final: 0.7710 (p0) REVERT: K 453 ASP cc_start: 0.5753 (p0) cc_final: 0.5500 (p0) REVERT: K 529 ASN cc_start: 0.7985 (m-40) cc_final: 0.7678 (m110) REVERT: L 451 ARG cc_start: 0.7639 (ptm-80) cc_final: 0.7397 (ttp-110) REVERT: L 461 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6863 (mmm160) REVERT: L 515 TYR cc_start: 0.7130 (m-80) cc_final: 0.6860 (m-80) REVERT: J 48 ASN cc_start: 0.7599 (m-40) cc_final: 0.7360 (m-40) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1333 time to fit residues: 79.6068 Evaluate side-chains 300 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 529 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN D 385 GLN D 545 ASN E 439 GLN E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN G 487 GLN G 493 GLN H 400 HIS ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN K 400 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.195880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136485 restraints weight = 32039.258| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.22 r_work: 0.3607 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 21330 Z= 0.282 Angle : 0.721 13.772 29179 Z= 0.373 Chirality : 0.050 0.460 3415 Planarity : 0.006 0.074 3712 Dihedral : 8.638 109.735 3075 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 11.34 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2592 helix: -0.14 (0.23), residues: 487 sheet: -0.13 (0.19), residues: 743 loop : -0.57 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 461 TYR 0.026 0.002 TYR M 337 PHE 0.024 0.003 PHE A 479 TRP 0.020 0.002 TRP F 382 HIS 0.012 0.002 HIS E 518 Details of bonding type rmsd covalent geometry : bond 0.00668 (21291) covalent geometry : angle 0.70845 (29089) SS BOND : bond 0.00555 ( 27) SS BOND : angle 0.98304 ( 54) hydrogen bonds : bond 0.04614 ( 598) hydrogen bonds : angle 6.01554 ( 1842) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 2.66192 ( 3) link_NAG-ASN : bond 0.00770 ( 11) link_NAG-ASN : angle 3.94840 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.7958 (m-80) cc_final: 0.7733 (m-80) REVERT: M 322 MET cc_start: 0.6798 (mmm) cc_final: 0.6488 (mmm) REVERT: M 418 TYR cc_start: 0.7727 (t80) cc_final: 0.7521 (t80) REVERT: A 570 ASP cc_start: 0.7986 (t70) cc_final: 0.7706 (t0) REVERT: B 419 ASN cc_start: 0.8677 (m110) cc_final: 0.8343 (p0) REVERT: C 461 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7330 (mtt180) REVERT: C 495 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8349 (mt) REVERT: C 506 MET cc_start: 0.8626 (mtm) cc_final: 0.8196 (mtp) REVERT: D 506 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8269 (mtm) REVERT: D 546 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.7047 (mtm180) REVERT: E 419 ASN cc_start: 0.8965 (m110) cc_final: 0.8639 (m110) REVERT: F 529 ASN cc_start: 0.7623 (m110) cc_final: 0.6916 (m-40) REVERT: G 455 TYR cc_start: 0.8306 (m-80) cc_final: 0.7632 (m-80) REVERT: G 467 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: G 506 MET cc_start: 0.8270 (pmm) cc_final: 0.8002 (pmm) REVERT: G 554 LYS cc_start: 0.7442 (mppt) cc_final: 0.6885 (mttt) REVERT: H 375 TYR cc_start: 0.4171 (t80) cc_final: 0.3910 (t80) REVERT: H 468 GLU cc_start: 0.8040 (tt0) cc_final: 0.7794 (tm-30) REVERT: H 529 ASN cc_start: 0.7907 (m-40) cc_final: 0.7446 (m-40) REVERT: K 414 CYS cc_start: 0.8170 (t) cc_final: 0.7400 (m) REVERT: K 449 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7268 (tp) REVERT: K 529 ASN cc_start: 0.8461 (m-40) cc_final: 0.8179 (m110) REVERT: L 461 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7456 (mmm-85) REVERT: L 515 TYR cc_start: 0.7766 (m-80) cc_final: 0.7104 (m-80) REVERT: J 51 ASP cc_start: 0.7213 (t70) cc_final: 0.6937 (t0) REVERT: J 109 TYR cc_start: 0.6941 (m-80) cc_final: 0.6718 (m-80) REVERT: J 117 TYR cc_start: 0.6505 (t80) cc_final: 0.6237 (t80) outliers start: 48 outliers final: 28 residues processed: 349 average time/residue: 0.1331 time to fit residues: 69.2177 Evaluate side-chains 303 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 530 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 350 ILE Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 66 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 ASN ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 402 ASN A 529 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN C 493 GLN D 385 GLN D 545 ASN E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN G 400 HIS G 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 HIS K 419 ASN ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.197214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.143796 restraints weight = 32096.220| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.43 r_work: 0.3612 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21330 Z= 0.136 Angle : 0.572 12.334 29179 Z= 0.291 Chirality : 0.045 0.450 3415 Planarity : 0.004 0.071 3712 Dihedral : 7.758 104.240 3075 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.07 % Allowed : 13.37 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2592 helix: 0.13 (0.23), residues: 493 sheet: -0.13 (0.19), residues: 727 loop : -0.49 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 491 TYR 0.029 0.001 TYR L 455 PHE 0.019 0.002 PHE M 346 TRP 0.019 0.001 TRP F 382 HIS 0.007 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00309 (21291) covalent geometry : angle 0.55883 (29089) SS BOND : bond 0.00226 ( 27) SS BOND : angle 0.65127 ( 54) hydrogen bonds : bond 0.03785 ( 598) hydrogen bonds : angle 5.59839 ( 1842) link_BETA1-4 : bond 0.01254 ( 1) link_BETA1-4 : angle 2.72671 ( 3) link_NAG-ASN : bond 0.00693 ( 11) link_NAG-ASN : angle 3.56181 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 288 time to evaluate : 0.516 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: M 235 TYR cc_start: 0.7952 (m-80) cc_final: 0.7726 (m-80) REVERT: M 322 MET cc_start: 0.6888 (mmm) cc_final: 0.6528 (mmm) REVERT: M 418 TYR cc_start: 0.7734 (t80) cc_final: 0.7473 (t80) REVERT: A 570 ASP cc_start: 0.7851 (t70) cc_final: 0.7630 (t0) REVERT: C 495 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 506 MET cc_start: 0.8589 (mtp) cc_final: 0.8325 (mtm) REVERT: E 419 ASN cc_start: 0.9006 (m110) cc_final: 0.8646 (m110) REVERT: G 455 TYR cc_start: 0.8239 (m-80) cc_final: 0.7528 (m-80) REVERT: G 489 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7482 (ptp) REVERT: G 554 LYS cc_start: 0.7516 (mppt) cc_final: 0.6979 (mttt) REVERT: H 375 TYR cc_start: 0.4410 (t80) cc_final: 0.4153 (t80) REVERT: H 468 GLU cc_start: 0.8055 (tt0) cc_final: 0.7847 (tp30) REVERT: H 529 ASN cc_start: 0.7983 (m-40) cc_final: 0.7501 (m-40) REVERT: K 410 GLU cc_start: 0.5643 (tm-30) cc_final: 0.5360 (tm-30) REVERT: K 414 CYS cc_start: 0.8111 (t) cc_final: 0.7407 (m) REVERT: K 461 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7177 (mtm-85) REVERT: K 529 ASN cc_start: 0.8445 (m-40) cc_final: 0.8176 (m-40) REVERT: K 553 ASP cc_start: 0.7759 (t0) cc_final: 0.7349 (t70) REVERT: L 461 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7386 (mmm-85) REVERT: L 471 THR cc_start: 0.8640 (m) cc_final: 0.8314 (t) REVERT: L 515 TYR cc_start: 0.7710 (m-80) cc_final: 0.7036 (m-80) REVERT: L 519 SER cc_start: 0.8289 (m) cc_final: 0.7376 (t) REVERT: J 117 TYR cc_start: 0.6356 (t80) cc_final: 0.6077 (t80) outliers start: 49 outliers final: 37 residues processed: 324 average time/residue: 0.1383 time to fit residues: 67.4607 Evaluate side-chains 303 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 450 HIS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 96 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN A 393 HIS A 490 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS F 439 GLN F 463 GLN F 487 GLN F 529 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.188704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127108 restraints weight = 32013.099| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.24 r_work: 0.3487 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21330 Z= 0.315 Angle : 0.707 12.979 29179 Z= 0.364 Chirality : 0.050 0.495 3415 Planarity : 0.005 0.070 3712 Dihedral : 7.675 99.932 3075 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.06 % Allowed : 14.89 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.83 (0.16), residues: 2592 helix: -0.01 (0.23), residues: 492 sheet: -0.51 (0.18), residues: 753 loop : -0.68 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 314 TYR 0.042 0.002 TYR L 455 PHE 0.028 0.003 PHE B 424 TRP 0.022 0.002 TRP F 382 HIS 0.038 0.002 HIS K 400 Details of bonding type rmsd covalent geometry : bond 0.00738 (21291) covalent geometry : angle 0.69558 (29089) SS BOND : bond 0.00569 ( 27) SS BOND : angle 0.87638 ( 54) hydrogen bonds : bond 0.04292 ( 598) hydrogen bonds : angle 5.88088 ( 1842) link_BETA1-4 : bond 0.00300 ( 1) link_BETA1-4 : angle 2.52255 ( 3) link_NAG-ASN : bond 0.00649 ( 11) link_NAG-ASN : angle 3.71758 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 297 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8278 (m-80) cc_final: 0.7901 (m-80) REVERT: M 322 MET cc_start: 0.6971 (mmm) cc_final: 0.6399 (mmm) REVERT: A 346 ARG cc_start: 0.5928 (tpm170) cc_final: 0.5420 (ptp-170) REVERT: A 361 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7126 (mttt) REVERT: B 419 ASN cc_start: 0.8540 (m110) cc_final: 0.8218 (p0) REVERT: B 570 ASP cc_start: 0.6510 (m-30) cc_final: 0.5748 (t0) REVERT: C 424 PHE cc_start: 0.6271 (m-10) cc_final: 0.5943 (m-10) REVERT: C 467 ARG cc_start: 0.7718 (mmt180) cc_final: 0.7401 (mmt180) REVERT: C 495 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8788 (mt) REVERT: E 419 ASN cc_start: 0.9080 (m110) cc_final: 0.8714 (m110) REVERT: E 568 MET cc_start: 0.6246 (tpt) cc_final: 0.5967 (tpp) REVERT: G 467 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7634 (mmm-85) REVERT: G 554 LYS cc_start: 0.7961 (mppt) cc_final: 0.7602 (mtpt) REVERT: H 375 TYR cc_start: 0.4637 (t80) cc_final: 0.4337 (t80) REVERT: H 468 GLU cc_start: 0.8190 (tt0) cc_final: 0.7943 (tp30) REVERT: H 529 ASN cc_start: 0.8097 (m-40) cc_final: 0.7567 (m-40) REVERT: K 529 ASN cc_start: 0.8430 (m-40) cc_final: 0.8194 (m110) REVERT: K 554 LYS cc_start: 0.8723 (tttt) cc_final: 0.8460 (tttt) REVERT: L 461 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: L 515 TYR cc_start: 0.7685 (m-80) cc_final: 0.6952 (m-80) REVERT: J 117 TYR cc_start: 0.7043 (t80) cc_final: 0.6774 (t80) outliers start: 96 outliers final: 64 residues processed: 374 average time/residue: 0.1364 time to fit residues: 76.1670 Evaluate side-chains 336 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 530 THR Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 485 PHE Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 112 optimal weight: 0.9990 chunk 231 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 161 optimal weight: 40.0000 chunk 249 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 529 ASN B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.192009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136549 restraints weight = 31636.587| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.45 r_work: 0.3543 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21330 Z= 0.136 Angle : 0.580 11.936 29179 Z= 0.296 Chirality : 0.046 0.458 3415 Planarity : 0.005 0.080 3712 Dihedral : 7.138 100.942 3075 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.05 % Allowed : 16.84 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.62 (0.16), residues: 2592 helix: 0.23 (0.23), residues: 489 sheet: -0.41 (0.18), residues: 746 loop : -0.56 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 491 TYR 0.030 0.001 TYR L 455 PHE 0.018 0.002 PHE H 424 TRP 0.026 0.001 TRP F 382 HIS 0.009 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00312 (21291) covalent geometry : angle 0.56661 (29089) SS BOND : bond 0.00252 ( 27) SS BOND : angle 0.65375 ( 54) hydrogen bonds : bond 0.03431 ( 598) hydrogen bonds : angle 5.41335 ( 1842) link_BETA1-4 : bond 0.01330 ( 1) link_BETA1-4 : angle 2.46951 ( 3) link_NAG-ASN : bond 0.00696 ( 11) link_NAG-ASN : angle 3.67119 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 291 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8180 (m-10) cc_final: 0.7931 (m-80) REVERT: M 322 MET cc_start: 0.7113 (mmm) cc_final: 0.6716 (mmm) REVERT: A 346 ARG cc_start: 0.5881 (tpm170) cc_final: 0.5388 (ptp-170) REVERT: A 361 LYS cc_start: 0.7397 (mmtt) cc_final: 0.7057 (mttt) REVERT: A 570 ASP cc_start: 0.8232 (t0) cc_final: 0.7927 (t0) REVERT: B 570 ASP cc_start: 0.6490 (m-30) cc_final: 0.5797 (t0) REVERT: C 495 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8634 (mt) REVERT: D 506 MET cc_start: 0.8515 (mtm) cc_final: 0.8193 (mtp) REVERT: E 419 ASN cc_start: 0.9040 (m110) cc_final: 0.8653 (m110) REVERT: E 455 TYR cc_start: 0.8695 (m-80) cc_final: 0.8463 (m-80) REVERT: E 568 MET cc_start: 0.6341 (tpt) cc_final: 0.6065 (tpp) REVERT: F 551 THR cc_start: 0.8794 (m) cc_final: 0.8579 (t) REVERT: G 364 LYS cc_start: 0.7473 (mmmt) cc_final: 0.7001 (tppt) REVERT: G 414 CYS cc_start: 0.6698 (OUTLIER) cc_final: 0.5785 (t) REVERT: G 455 TYR cc_start: 0.8407 (m-80) cc_final: 0.7718 (m-80) REVERT: G 467 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7636 (mmm-85) REVERT: G 489 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7502 (ptp) REVERT: G 526 GLU cc_start: 0.7621 (mp0) cc_final: 0.7310 (mp0) REVERT: G 554 LYS cc_start: 0.7831 (mppt) cc_final: 0.7323 (mtpt) REVERT: H 375 TYR cc_start: 0.4594 (t80) cc_final: 0.4284 (t80) REVERT: H 468 GLU cc_start: 0.8195 (tt0) cc_final: 0.7960 (tp30) REVERT: H 529 ASN cc_start: 0.8232 (m-40) cc_final: 0.7723 (m-40) REVERT: K 529 ASN cc_start: 0.8400 (m-40) cc_final: 0.8176 (m-40) REVERT: L 487 GLN cc_start: 0.6391 (mt0) cc_final: 0.5859 (mm110) REVERT: L 515 TYR cc_start: 0.7690 (m-80) cc_final: 0.6926 (m-80) REVERT: L 519 SER cc_start: 0.8419 (m) cc_final: 0.7581 (t) REVERT: J 117 TYR cc_start: 0.6750 (t80) cc_final: 0.6402 (t80) outliers start: 72 outliers final: 49 residues processed: 346 average time/residue: 0.1307 time to fit residues: 67.7839 Evaluate side-chains 322 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 414 CYS Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 555 SER Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 183 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 256 optimal weight: 0.3980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 326 GLN A 400 HIS A 529 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN C 465 ASN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.192300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.138152 restraints weight = 31541.513| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.62 r_work: 0.3529 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21330 Z= 0.158 Angle : 0.585 11.970 29179 Z= 0.298 Chirality : 0.046 0.441 3415 Planarity : 0.005 0.076 3712 Dihedral : 6.827 100.668 3075 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.81 % Allowed : 16.79 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2592 helix: 0.29 (0.23), residues: 491 sheet: -0.41 (0.18), residues: 744 loop : -0.53 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 491 TYR 0.027 0.001 TYR L 455 PHE 0.036 0.002 PHE F 405 TRP 0.021 0.001 TRP F 382 HIS 0.014 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00370 (21291) covalent geometry : angle 0.57282 (29089) SS BOND : bond 0.00284 ( 27) SS BOND : angle 0.59424 ( 54) hydrogen bonds : bond 0.03380 ( 598) hydrogen bonds : angle 5.35093 ( 1842) link_BETA1-4 : bond 0.00223 ( 1) link_BETA1-4 : angle 2.17259 ( 3) link_NAG-ASN : bond 0.00621 ( 11) link_NAG-ASN : angle 3.57058 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 278 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8209 (m-10) cc_final: 0.7966 (m-80) REVERT: M 322 MET cc_start: 0.7124 (mmm) cc_final: 0.6746 (mmm) REVERT: A 361 LYS cc_start: 0.7401 (mmtt) cc_final: 0.7041 (mttt) REVERT: A 570 ASP cc_start: 0.8295 (t0) cc_final: 0.7924 (t0) REVERT: B 419 ASN cc_start: 0.8640 (m110) cc_final: 0.8307 (p0) REVERT: B 570 ASP cc_start: 0.6488 (m-30) cc_final: 0.5849 (t0) REVERT: D 506 MET cc_start: 0.8478 (mtm) cc_final: 0.8153 (mtp) REVERT: E 419 ASN cc_start: 0.8985 (m110) cc_final: 0.8598 (m110) REVERT: E 455 TYR cc_start: 0.8736 (m-80) cc_final: 0.8462 (m-80) REVERT: E 553 ASP cc_start: 0.7759 (m-30) cc_final: 0.7095 (m-30) REVERT: E 568 MET cc_start: 0.6294 (tpt) cc_final: 0.6016 (tpp) REVERT: F 551 THR cc_start: 0.8806 (m) cc_final: 0.8585 (t) REVERT: G 364 LYS cc_start: 0.7508 (mmmt) cc_final: 0.7016 (tppt) REVERT: G 455 TYR cc_start: 0.8356 (m-80) cc_final: 0.7651 (m-80) REVERT: G 467 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7540 (mmm-85) REVERT: G 489 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7486 (ptp) REVERT: G 554 LYS cc_start: 0.7862 (mppt) cc_final: 0.7375 (mttt) REVERT: H 468 GLU cc_start: 0.8225 (tt0) cc_final: 0.7971 (tp30) REVERT: H 529 ASN cc_start: 0.8264 (m-40) cc_final: 0.7757 (m-40) REVERT: K 529 ASN cc_start: 0.8364 (m-40) cc_final: 0.8103 (m-40) REVERT: L 515 TYR cc_start: 0.7645 (m-80) cc_final: 0.6856 (m-80) REVERT: L 519 SER cc_start: 0.8514 (m) cc_final: 0.7608 (t) REVERT: L 534 TYR cc_start: 0.7400 (m-80) cc_final: 0.7102 (m-80) REVERT: L 553 ASP cc_start: 0.6968 (m-30) cc_final: 0.6723 (m-30) REVERT: J 41 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8847 (m) REVERT: J 117 TYR cc_start: 0.6858 (t80) cc_final: 0.6498 (t80) outliers start: 90 outliers final: 64 residues processed: 345 average time/residue: 0.1391 time to fit residues: 71.8145 Evaluate side-chains 337 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 41 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 212 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** 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 = 0.4425 r_free = 0.4425 target = 0.191271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135565 restraints weight = 31617.025| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.59 r_work: 0.3506 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21330 Z= 0.176 Angle : 0.590 11.977 29179 Z= 0.300 Chirality : 0.046 0.437 3415 Planarity : 0.005 0.081 3712 Dihedral : 6.699 100.748 3075 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.89 % Allowed : 17.39 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.62 (0.16), residues: 2592 helix: 0.31 (0.23), residues: 491 sheet: -0.48 (0.18), residues: 758 loop : -0.54 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 491 TYR 0.031 0.002 TYR H 375 PHE 0.028 0.002 PHE F 405 TRP 0.025 0.001 TRP F 382 HIS 0.008 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00415 (21291) covalent geometry : angle 0.57704 (29089) SS BOND : bond 0.00302 ( 27) SS BOND : angle 0.62397 ( 54) hydrogen bonds : bond 0.03422 ( 598) hydrogen bonds : angle 5.32648 ( 1842) link_BETA1-4 : bond 0.00772 ( 1) link_BETA1-4 : angle 2.13467 ( 3) link_NAG-ASN : bond 0.00564 ( 11) link_NAG-ASN : angle 3.65004 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 278 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8217 (m-10) cc_final: 0.7989 (m-80) REVERT: M 300 ASN cc_start: 0.8409 (t0) cc_final: 0.8065 (t0) REVERT: A 361 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7139 (mttt) REVERT: B 419 ASN cc_start: 0.8600 (m110) cc_final: 0.8253 (p0) REVERT: E 419 ASN cc_start: 0.8989 (m110) cc_final: 0.8583 (m110) REVERT: E 455 TYR cc_start: 0.8721 (m-80) cc_final: 0.8445 (m-80) REVERT: E 553 ASP cc_start: 0.7809 (m-30) cc_final: 0.7181 (m-30) REVERT: F 551 THR cc_start: 0.8865 (m) cc_final: 0.8645 (t) REVERT: G 467 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7217 (mmm-85) REVERT: G 489 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7478 (ptp) REVERT: G 554 LYS cc_start: 0.7890 (mppt) cc_final: 0.7427 (mtpt) REVERT: H 468 GLU cc_start: 0.8252 (tt0) cc_final: 0.7949 (tp30) REVERT: H 529 ASN cc_start: 0.8313 (m-40) cc_final: 0.7883 (m-40) REVERT: H 568 MET cc_start: 0.6565 (mpp) cc_final: 0.6268 (mmt) REVERT: K 529 ASN cc_start: 0.8378 (m-40) cc_final: 0.8079 (m-40) REVERT: L 487 GLN cc_start: 0.6322 (mt0) cc_final: 0.5899 (mm110) REVERT: L 515 TYR cc_start: 0.7616 (m-80) cc_final: 0.6855 (m-80) REVERT: L 519 SER cc_start: 0.8435 (m) cc_final: 0.7518 (t) REVERT: L 534 TYR cc_start: 0.7422 (m-80) cc_final: 0.7119 (m-80) REVERT: L 553 ASP cc_start: 0.7060 (m-30) cc_final: 0.6776 (m-30) REVERT: J 41 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (m) REVERT: J 46 ARG cc_start: 0.7713 (mmt180) cc_final: 0.7467 (mmt180) REVERT: J 117 TYR cc_start: 0.6979 (t80) cc_final: 0.6610 (t80) outliers start: 92 outliers final: 72 residues processed: 350 average time/residue: 0.1371 time to fit residues: 71.9189 Evaluate side-chains 341 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 267 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 41 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 119 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 90 optimal weight: 0.0370 chunk 135 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 220 optimal weight: 0.0070 chunk 230 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 142 optimal weight: 9.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS B 393 HIS B 463 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.191513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134744 restraints weight = 30836.881| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.07 r_work: 0.3576 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21330 Z= 0.115 Angle : 0.569 12.259 29179 Z= 0.287 Chirality : 0.045 0.406 3415 Planarity : 0.004 0.080 3712 Dihedral : 6.305 100.508 3075 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.30 % Allowed : 18.49 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.46 (0.16), residues: 2592 helix: 0.41 (0.23), residues: 491 sheet: -0.29 (0.19), residues: 735 loop : -0.48 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 491 TYR 0.026 0.001 TYR L 455 PHE 0.027 0.001 PHE F 405 TRP 0.025 0.001 TRP F 382 HIS 0.006 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00264 (21291) covalent geometry : angle 0.55606 (29089) SS BOND : bond 0.00217 ( 27) SS BOND : angle 0.49707 ( 54) hydrogen bonds : bond 0.03142 ( 598) hydrogen bonds : angle 5.10544 ( 1842) link_BETA1-4 : bond 0.01097 ( 1) link_BETA1-4 : angle 2.47833 ( 3) link_NAG-ASN : bond 0.00573 ( 11) link_NAG-ASN : angle 3.52419 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 235 TYR cc_start: 0.8219 (m-10) cc_final: 0.8016 (m-80) REVERT: M 300 ASN cc_start: 0.8423 (t0) cc_final: 0.8201 (t0) REVERT: A 361 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7128 (mttt) REVERT: A 499 LYS cc_start: 0.9190 (tttm) cc_final: 0.8917 (tttm) REVERT: A 534 TYR cc_start: 0.7858 (m-80) cc_final: 0.7634 (m-80) REVERT: A 570 ASP cc_start: 0.8073 (t0) cc_final: 0.7809 (t0) REVERT: B 419 ASN cc_start: 0.8590 (m110) cc_final: 0.8216 (p0) REVERT: B 443 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7108 (ttm110) REVERT: B 451 ARG cc_start: 0.8690 (ptm-80) cc_final: 0.8394 (ptm-80) REVERT: C 358 PHE cc_start: 0.8377 (t80) cc_final: 0.7764 (t80) REVERT: D 506 MET cc_start: 0.8392 (mtm) cc_final: 0.8057 (mtp) REVERT: E 419 ASN cc_start: 0.8953 (m110) cc_final: 0.8588 (m110) REVERT: E 455 TYR cc_start: 0.8646 (m-80) cc_final: 0.8395 (m-80) REVERT: E 553 ASP cc_start: 0.7797 (m-30) cc_final: 0.7314 (m-30) REVERT: F 551 THR cc_start: 0.8626 (m) cc_final: 0.8421 (t) REVERT: G 455 TYR cc_start: 0.8266 (m-80) cc_final: 0.7478 (m-80) REVERT: G 467 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7352 (mmm-85) REVERT: G 489 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7470 (ptp) REVERT: G 554 LYS cc_start: 0.7736 (mppt) cc_final: 0.7319 (mtpt) REVERT: H 375 TYR cc_start: 0.4516 (t80) cc_final: 0.4311 (t80) REVERT: H 529 ASN cc_start: 0.8261 (m-40) cc_final: 0.7815 (m110) REVERT: H 568 MET cc_start: 0.6556 (mpp) cc_final: 0.6297 (mmt) REVERT: K 529 ASN cc_start: 0.8323 (m-40) cc_final: 0.8066 (m-40) REVERT: L 487 GLN cc_start: 0.6261 (mt0) cc_final: 0.5839 (mm110) REVERT: L 515 TYR cc_start: 0.7582 (m-80) cc_final: 0.6771 (m-80) REVERT: L 534 TYR cc_start: 0.7367 (m-80) cc_final: 0.7113 (m-80) REVERT: J 41 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8799 (m) REVERT: J 46 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7432 (mmt180) REVERT: J 117 TYR cc_start: 0.6693 (t80) cc_final: 0.6375 (t80) outliers start: 78 outliers final: 60 residues processed: 342 average time/residue: 0.1271 time to fit residues: 66.4049 Evaluate side-chains 327 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.190617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135111 restraints weight = 31598.564| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.46 r_work: 0.3504 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21330 Z= 0.181 Angle : 0.609 11.238 29179 Z= 0.308 Chirality : 0.046 0.426 3415 Planarity : 0.005 0.081 3712 Dihedral : 6.268 100.469 3075 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.26 % Allowed : 18.74 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.53 (0.16), residues: 2592 helix: 0.38 (0.23), residues: 491 sheet: -0.32 (0.18), residues: 737 loop : -0.55 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 491 TYR 0.029 0.001 TYR L 455 PHE 0.030 0.002 PHE E 354 TRP 0.029 0.001 TRP F 382 HIS 0.005 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00428 (21291) covalent geometry : angle 0.59735 (29089) SS BOND : bond 0.00323 ( 27) SS BOND : angle 0.55402 ( 54) hydrogen bonds : bond 0.03438 ( 598) hydrogen bonds : angle 5.26700 ( 1842) link_BETA1-4 : bond 0.00995 ( 1) link_BETA1-4 : angle 2.44928 ( 3) link_NAG-ASN : bond 0.00537 ( 11) link_NAG-ASN : angle 3.50729 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 279 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 235 TYR cc_start: 0.8248 (m-10) cc_final: 0.8008 (m-80) REVERT: M 300 ASN cc_start: 0.8437 (t0) cc_final: 0.8088 (t0) REVERT: A 361 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7083 (mttt) REVERT: A 570 ASP cc_start: 0.8153 (t0) cc_final: 0.7820 (t0) REVERT: B 443 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7219 (ttm110) REVERT: B 451 ARG cc_start: 0.8791 (ptm-80) cc_final: 0.8474 (ptp90) REVERT: C 376 ASP cc_start: 0.5026 (m-30) cc_final: 0.4806 (m-30) REVERT: D 506 MET cc_start: 0.8456 (mtm) cc_final: 0.8120 (mtp) REVERT: E 419 ASN cc_start: 0.8966 (m110) cc_final: 0.8566 (m110) REVERT: E 455 TYR cc_start: 0.8700 (m-80) cc_final: 0.8466 (m-80) REVERT: E 553 ASP cc_start: 0.7938 (m-30) cc_final: 0.7418 (m-30) REVERT: F 467 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7968 (mmm-85) REVERT: F 551 THR cc_start: 0.8891 (m) cc_final: 0.8677 (t) REVERT: G 467 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7295 (mmm-85) REVERT: G 489 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7411 (ptp) REVERT: G 554 LYS cc_start: 0.7888 (mppt) cc_final: 0.7472 (mtpt) REVERT: H 529 ASN cc_start: 0.8312 (m-40) cc_final: 0.7865 (m-40) REVERT: H 568 MET cc_start: 0.6678 (mpp) cc_final: 0.6395 (mmt) REVERT: K 529 ASN cc_start: 0.8317 (m-40) cc_final: 0.8110 (m-40) REVERT: L 487 GLN cc_start: 0.6263 (mt0) cc_final: 0.5815 (mm110) REVERT: L 515 TYR cc_start: 0.7587 (m-80) cc_final: 0.6672 (m-80) REVERT: L 534 TYR cc_start: 0.7394 (m-80) cc_final: 0.7162 (m-80) REVERT: J 41 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8840 (m) REVERT: J 46 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7554 (mmt180) REVERT: J 47 GLU cc_start: 0.8219 (mp0) cc_final: 0.7411 (mp0) REVERT: J 117 TYR cc_start: 0.6945 (t80) cc_final: 0.6569 (t80) outliers start: 77 outliers final: 66 residues processed: 338 average time/residue: 0.1288 time to fit residues: 65.6040 Evaluate side-chains 337 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 233 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 254 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 490 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.191888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132165 restraints weight = 31497.670| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.19 r_work: 0.3563 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21330 Z= 0.123 Angle : 0.594 10.688 29179 Z= 0.301 Chirality : 0.045 0.392 3415 Planarity : 0.004 0.081 3712 Dihedral : 6.044 100.052 3075 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.00 % Allowed : 19.33 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.39 (0.16), residues: 2592 helix: 0.45 (0.24), residues: 491 sheet: -0.24 (0.19), residues: 734 loop : -0.44 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 491 TYR 0.032 0.001 TYR H 375 PHE 0.027 0.001 PHE E 354 TRP 0.032 0.001 TRP F 382 HIS 0.005 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00283 (21291) covalent geometry : angle 0.58255 (29089) SS BOND : bond 0.00224 ( 27) SS BOND : angle 0.49599 ( 54) hydrogen bonds : bond 0.03187 ( 598) hydrogen bonds : angle 5.08204 ( 1842) link_BETA1-4 : bond 0.01133 ( 1) link_BETA1-4 : angle 2.65878 ( 3) link_NAG-ASN : bond 0.00534 ( 11) link_NAG-ASN : angle 3.40583 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8217 (m-10) cc_final: 0.7999 (m-80) REVERT: M 300 ASN cc_start: 0.8436 (t0) cc_final: 0.8186 (t0) REVERT: A 361 LYS cc_start: 0.7449 (mmtt) cc_final: 0.7031 (mttt) REVERT: A 499 LYS cc_start: 0.9213 (tttm) cc_final: 0.8918 (tttm) REVERT: A 534 TYR cc_start: 0.7870 (m-80) cc_final: 0.7623 (m-80) REVERT: A 545 ASN cc_start: 0.7882 (m-40) cc_final: 0.7681 (t0) REVERT: A 570 ASP cc_start: 0.8118 (t0) cc_final: 0.7816 (t0) REVERT: B 361 LYS cc_start: 0.7831 (mttm) cc_final: 0.7615 (mttm) REVERT: B 419 ASN cc_start: 0.8553 (m110) cc_final: 0.8188 (p0) REVERT: B 443 ARG cc_start: 0.7419 (ttm110) cc_final: 0.7147 (ttm110) REVERT: B 451 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8455 (ptm-80) REVERT: C 376 ASP cc_start: 0.4841 (m-30) cc_final: 0.4629 (m-30) REVERT: D 506 MET cc_start: 0.8388 (mtm) cc_final: 0.8047 (mtp) REVERT: E 419 ASN cc_start: 0.8972 (m110) cc_final: 0.8607 (m110) REVERT: E 455 TYR cc_start: 0.8610 (m-80) cc_final: 0.8365 (m-80) REVERT: E 553 ASP cc_start: 0.7861 (m-30) cc_final: 0.7346 (m-30) REVERT: F 467 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7822 (mmm-85) REVERT: F 551 THR cc_start: 0.8750 (m) cc_final: 0.8541 (t) REVERT: G 455 TYR cc_start: 0.8248 (m-80) cc_final: 0.7471 (m-80) REVERT: G 483 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8395 (t0) REVERT: G 489 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7363 (ptp) REVERT: G 554 LYS cc_start: 0.7683 (mppt) cc_final: 0.7246 (mtpt) REVERT: H 529 ASN cc_start: 0.8303 (m-40) cc_final: 0.7816 (m110) REVERT: H 568 MET cc_start: 0.6517 (mpp) cc_final: 0.6249 (mmt) REVERT: L 487 GLN cc_start: 0.6184 (mt0) cc_final: 0.5725 (mm110) REVERT: L 515 TYR cc_start: 0.7534 (m-80) cc_final: 0.6685 (m-80) REVERT: L 534 TYR cc_start: 0.7333 (m-80) cc_final: 0.7068 (m-80) REVERT: J 41 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8804 (m) REVERT: J 47 GLU cc_start: 0.8138 (mp0) cc_final: 0.7410 (mp0) REVERT: J 117 TYR cc_start: 0.6826 (t80) cc_final: 0.6480 (t80) outliers start: 71 outliers final: 66 residues processed: 334 average time/residue: 0.1477 time to fit residues: 73.5245 Evaluate side-chains 339 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 270 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 193 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 159 optimal weight: 0.0000 chunk 96 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.191198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131381 restraints weight = 31503.385| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.18 r_work: 0.3533 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21330 Z= 0.162 Angle : 0.605 10.871 29179 Z= 0.306 Chirality : 0.046 0.412 3415 Planarity : 0.004 0.084 3712 Dihedral : 6.030 99.937 3075 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.17 % Allowed : 19.12 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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 aren not related in a simple way. whole: -0.48 (0.16), residues: 2592 helix: 0.40 (0.23), residues: 491 sheet: -0.30 (0.18), residues: 743 loop : -0.50 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 491 TYR 0.033 0.001 TYR H 375 PHE 0.025 0.002 PHE E 354 TRP 0.030 0.001 TRP F 382 HIS 0.007 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00383 (21291) covalent geometry : angle 0.59411 (29089) SS BOND : bond 0.00274 ( 27) SS BOND : angle 0.50981 ( 54) hydrogen bonds : bond 0.03321 ( 598) hydrogen bonds : angle 5.16407 ( 1842) link_BETA1-4 : bond 0.01126 ( 1) link_BETA1-4 : angle 2.52088 ( 3) link_NAG-ASN : bond 0.00530 ( 11) link_NAG-ASN : angle 3.42631 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4843.54 seconds wall clock time: 83 minutes 46.27 seconds (5026.27 seconds total)