Starting phenix.real_space_refine on Sat Jul 4 18:21:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_33805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_33805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_33805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_33805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_33805.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_33805.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yg2_33805/07_2026/7yg2_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 5.51, per 1000 atoms: 0.27 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: 1.83 Conformation dependent library (CDL) restraints added in 832.7 milliseconds 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: 0.68 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: 3.91 Time building geometry restraints manager: 2.42 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 - 17.97: 11614 17.97 - 35.94: 1027 35.94 - 53.92: 173 53.92 - 71.89: 36 71.89 - 89.86: 15 Dihedral angle restraints: 12865 sinusoidal: 5117 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 12862 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.020 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 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 : 13.865 89.860 7726 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 are 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/Z covalent geometry : bond 0.00292 / 0.14 (21291) covalent geometry : angle 0.60835 / 0.32 (29089) SS BOND : bond 0.00216 / 0.12 ( 27) SS BOND : angle 0.85500 / 0.60 ( 54) hydrogen bonds : bond 0.23920 / 15.73 ( 598) hydrogen bonds : angle 9.24349 / 6.78 ( 1842) link_BETA1-4 : bond 0.01421 / 0.75 ( 1) link_BETA1-4 : angle 1.14811 / 0.60 ( 3) link_NAG-ASN : bond 0.00725 / 0.39 ( 11) link_NAG-ASN : angle 4.18640 / 2.57 ( 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 : 0.627 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: 0.6813 (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: 0.1543 time to fit residues: 92.6707 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 : 0.774 ------------------------------------------------------------------------------- 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... M 194 ASN ** 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 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 518 HIS ** 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.196419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138655 restraints weight = 32060.626| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.45 r_work: 0.3609 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21330 Z= 0.274 Angle : 0.698 13.715 29179 Z= 0.363 Chirality : 0.050 0.442 3415 Planarity : 0.005 0.076 3712 Dihedral : 4.312 26.359 2823 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.99 % Allowed : 11.04 % Favored : 86.97 % 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 are not related in a simple way. whole: -0.56 (0.16), residues: 2592 helix: -0.10 (0.23), residues: 487 sheet: -0.07 (0.19), residues: 741 loop : -0.56 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 461 TYR 0.037 0.002 TYR J 109 PHE 0.023 0.003 PHE A 479 TRP 0.018 0.002 TRP C 418 HIS 0.011 0.001 HIS E 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.27 (21291) covalent geometry : angle 0.68501 / 0.36 (29089) SS BOND : bond 0.00561 / 0.37 ( 27) SS BOND : angle 1.06829 / 0.76 ( 54) hydrogen bonds : bond 0.04730 / 3.03 ( 598) hydrogen bonds : angle 6.07745 / 4.44 ( 1842) link_BETA1-4 : bond 0.00040 / 0.02 ( 1) link_BETA1-4 : angle 1.29178 / 0.68 ( 3) link_NAG-ASN : bond 0.00740 / 0.29 ( 11) link_NAG-ASN : angle 3.86198 / 2.38 ( 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 366 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 319 time to evaluate : 0.786 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: 0.7960 (m-80) cc_final: 0.7709 (m-80) REVERT: M 322 MET cc_start: 0.6803 (mmm) cc_final: 0.6498 (mmm) REVERT: M 418 TYR cc_start: 0.7707 (t80) cc_final: 0.7496 (t80) REVERT: A 570 ASP cc_start: 0.8002 (t70) cc_final: 0.7746 (t0) REVERT: B 419 ASN cc_start: 0.8677 (m110) cc_final: 0.8342 (p0) REVERT: B 541 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: C 495 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 506 MET cc_start: 0.8657 (mtm) cc_final: 0.8232 (mtp) REVERT: D 506 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8344 (mtm) REVERT: D 546 ARG cc_start: 0.7339 (ttp-110) cc_final: 0.7103 (mtm180) REVERT: E 419 ASN cc_start: 0.8948 (m110) cc_final: 0.8613 (m110) REVERT: F 529 ASN cc_start: 0.7627 (m110) cc_final: 0.6960 (m-40) REVERT: G 455 TYR cc_start: 0.8319 (m-80) cc_final: 0.7607 (m-80) REVERT: G 467 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: G 506 MET cc_start: 0.8353 (pmm) cc_final: 0.8101 (pmm) REVERT: G 554 LYS cc_start: 0.7492 (mppt) cc_final: 0.6929 (mttt) REVERT: H 375 TYR cc_start: 0.4189 (t80) cc_final: 0.3935 (t80) REVERT: H 468 GLU cc_start: 0.8006 (tt0) cc_final: 0.7777 (tm-30) REVERT: H 529 ASN cc_start: 0.7909 (m-40) cc_final: 0.7451 (m-40) REVERT: K 414 CYS cc_start: 0.8109 (t) cc_final: 0.7475 (m) REVERT: K 529 ASN cc_start: 0.8442 (m-40) cc_final: 0.8176 (m-40) REVERT: L 461 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: L 515 TYR cc_start: 0.7763 (m-80) cc_final: 0.7115 (m-80) REVERT: J 117 TYR cc_start: 0.6504 (t80) cc_final: 0.6258 (t80) outliers start: 47 outliers final: 28 residues processed: 349 average time/residue: 0.1658 time to fit residues: 86.1140 Evaluate side-chains 296 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 B residue 541 GLU 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 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: 0.8980 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 196 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 402 ASN A 529 ASN B 395 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** F 463 GLN G 400 HIS G 529 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 HIS ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.198025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.144943 restraints weight = 32143.835| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.87 r_work: 0.3627 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21330 Z= 0.126 Angle : 0.562 12.186 29179 Z= 0.287 Chirality : 0.045 0.440 3415 Planarity : 0.004 0.070 3712 Dihedral : 4.014 28.901 2823 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.99 % Allowed : 13.28 % Favored : 84.73 % 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 are not related in a simple way. whole: -0.43 (0.16), residues: 2592 helix: 0.16 (0.23), residues: 493 sheet: -0.07 (0.19), residues: 725 loop : -0.47 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 491 TYR 0.027 0.001 TYR L 455 PHE 0.025 0.002 PHE B 424 TRP 0.021 0.001 TRP F 382 HIS 0.008 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (21291) covalent geometry : angle 0.54962 / 0.28 (29089) SS BOND : bond 0.00204 / 0.14 ( 27) SS BOND : angle 0.64305 / 0.44 ( 54) hydrogen bonds : bond 0.03780 / 2.44 ( 598) hydrogen bonds : angle 5.57599 / 4.09 ( 1842) link_BETA1-4 : bond 0.01084 / 0.57 ( 1) link_BETA1-4 : angle 1.13834 / 0.60 ( 3) link_NAG-ASN : bond 0.00665 / 0.45 ( 11) link_NAG-ASN : angle 3.45395 / 2.13 ( 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 336 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 0.723 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 322 MET cc_start: 0.6886 (mmm) cc_final: 0.6519 (mmm) REVERT: A 534 TYR cc_start: 0.7924 (m-80) cc_final: 0.7687 (m-80) REVERT: A 570 ASP cc_start: 0.7857 (t70) cc_final: 0.7627 (t0) REVERT: D 506 MET cc_start: 0.8563 (mtp) cc_final: 0.8293 (mtm) REVERT: E 419 ASN cc_start: 0.9002 (m110) cc_final: 0.8643 (m110) REVERT: G 455 TYR cc_start: 0.8205 (m-80) cc_final: 0.7510 (m-80) REVERT: G 489 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7403 (ptp) REVERT: G 554 LYS cc_start: 0.7493 (mppt) cc_final: 0.6946 (mttt) REVERT: H 375 TYR cc_start: 0.4423 (t80) cc_final: 0.4172 (t80) REVERT: H 468 GLU cc_start: 0.8050 (tt0) cc_final: 0.7769 (tm-30) REVERT: H 529 ASN cc_start: 0.7992 (m-40) cc_final: 0.7506 (m-40) REVERT: K 410 GLU cc_start: 0.5632 (tm-30) cc_final: 0.5347 (tm-30) REVERT: K 414 CYS cc_start: 0.8099 (t) cc_final: 0.7382 (m) REVERT: K 449 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6938 (mp) REVERT: K 461 ARG cc_start: 0.7731 (mtm180) cc_final: 0.7151 (mtm-85) REVERT: K 529 ASN cc_start: 0.8444 (m-40) cc_final: 0.8172 (m-40) REVERT: L 461 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: L 471 THR cc_start: 0.8602 (m) cc_final: 0.8278 (t) REVERT: L 515 TYR cc_start: 0.7727 (m-80) cc_final: 0.7142 (m-80) REVERT: L 519 SER cc_start: 0.8271 (m) cc_final: 0.7377 (t) REVERT: J 117 TYR cc_start: 0.6344 (t80) cc_final: 0.6079 (t80) outliers start: 47 outliers final: 34 residues processed: 321 average time/residue: 0.1592 time to fit residues: 76.9426 Evaluate side-chains 301 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR 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 547 VAL Chi-restraints excluded: chain D residue 564 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 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 449 LEU 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 571 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 96 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 246 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 154 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN A 393 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 419 ASN B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS F 439 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 419 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.192262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136720 restraints weight = 31925.133| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.89 r_work: 0.3536 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21330 Z= 0.226 Angle : 0.619 12.175 29179 Z= 0.319 Chirality : 0.047 0.459 3415 Planarity : 0.005 0.067 3712 Dihedral : 4.244 30.660 2823 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.43 % Allowed : 14.89 % Favored : 81.68 % 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 are not related in a simple way. whole: -0.52 (0.16), residues: 2592 helix: 0.27 (0.23), residues: 492 sheet: -0.26 (0.19), residues: 735 loop : -0.54 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 491 TYR 0.037 0.002 TYR L 455 PHE 0.025 0.002 PHE M 346 TRP 0.019 0.002 TRP F 382 HIS 0.033 0.001 HIS K 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (21291) covalent geometry : angle 0.60896 / 0.32 (29089) SS BOND : bond 0.00372 / 0.22 ( 27) SS BOND : angle 0.68116 / 0.46 ( 54) hydrogen bonds : bond 0.03810 / 2.44 ( 598) hydrogen bonds : angle 5.57527 / 4.08 ( 1842) link_BETA1-4 : bond 0.00618 / 0.33 ( 1) link_BETA1-4 : angle 1.03563 / 0.55 ( 3) link_NAG-ASN : bond 0.00571 / 0.30 ( 11) link_NAG-ASN : angle 3.40188 / 2.08 ( 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 367 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 286 time to evaluate : 0.804 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 322 MET cc_start: 0.6967 (mmm) cc_final: 0.6648 (mmm) REVERT: A 346 ARG cc_start: 0.5876 (tpm170) cc_final: 0.5412 (ptp-170) REVERT: A 361 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6993 (mttt) REVERT: A 570 ASP cc_start: 0.8064 (t70) cc_final: 0.7818 (t0) REVERT: B 419 ASN cc_start: 0.8540 (m110) cc_final: 0.8205 (p0) REVERT: B 570 ASP cc_start: 0.6443 (m-30) cc_final: 0.5585 (t0) REVERT: C 424 PHE cc_start: 0.6242 (m-10) cc_final: 0.5929 (m-10) REVERT: D 506 MET cc_start: 0.8590 (mtp) cc_final: 0.8378 (mtm) REVERT: E 419 ASN cc_start: 0.9058 (m110) cc_final: 0.8694 (m110) REVERT: G 455 TYR cc_start: 0.8428 (m-80) cc_final: 0.7775 (m-80) REVERT: G 467 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7571 (mmm-85) REVERT: G 554 LYS cc_start: 0.7822 (mppt) cc_final: 0.7417 (mtpt) REVERT: H 375 TYR cc_start: 0.4565 (t80) cc_final: 0.4271 (t80) REVERT: H 468 GLU cc_start: 0.8166 (tt0) cc_final: 0.7906 (tp30) REVERT: H 529 ASN cc_start: 0.8173 (m-40) cc_final: 0.7653 (m-40) REVERT: K 461 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7212 (mtm-85) REVERT: K 529 ASN cc_start: 0.8433 (m-40) cc_final: 0.8229 (m-40) REVERT: K 553 ASP cc_start: 0.8019 (t0) cc_final: 0.7818 (t0) REVERT: K 554 LYS cc_start: 0.8350 (tttt) cc_final: 0.8140 (tttt) REVERT: L 471 THR cc_start: 0.8945 (m) cc_final: 0.8569 (t) REVERT: L 515 TYR cc_start: 0.7693 (m-80) cc_final: 0.6946 (m-80) REVERT: J 51 ASP cc_start: 0.7979 (t70) cc_final: 0.7675 (t0) REVERT: J 117 TYR cc_start: 0.6810 (t80) cc_final: 0.6549 (t80) outliers start: 81 outliers final: 57 residues processed: 348 average time/residue: 0.1623 time to fit residues: 84.5775 Evaluate side-chains 326 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 476 VAL Chi-restraints excluded: chain D residue 419 ASN 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 564 VAL 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 E residue 551 THR 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 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 H residue 567 VAL 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 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 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 L residue 571 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 112 optimal weight: 3.9990 chunk 231 optimal weight: 0.2980 chunk 207 optimal weight: 7.9990 chunk 255 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 249 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 439 GLN B 463 GLN B 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 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN K 400 HIS ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.194707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.140963 restraints weight = 31707.695| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.61 r_work: 0.3573 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3683 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= 0.118 Angle : 0.553 11.613 29179 Z= 0.282 Chirality : 0.045 0.441 3415 Planarity : 0.004 0.074 3712 Dihedral : 4.043 33.577 2823 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.75 % Allowed : 16.62 % Favored : 80.63 % 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 are not related in a simple way. whole: -0.38 (0.16), residues: 2592 helix: 0.41 (0.24), residues: 490 sheet: -0.21 (0.19), residues: 728 loop : -0.42 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 491 TYR 0.029 0.001 TYR L 455 PHE 0.018 0.001 PHE H 424 TRP 0.025 0.001 TRP F 382 HIS 0.007 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21291) covalent geometry : angle 0.54209 / 0.28 (29089) SS BOND : bond 0.00203 / 0.13 ( 27) SS BOND : angle 0.50339 / 0.34 ( 54) hydrogen bonds : bond 0.03262 / 2.10 ( 598) hydrogen bonds : angle 5.27062 / 3.87 ( 1842) link_BETA1-4 : bond 0.00761 / 0.40 ( 1) link_BETA1-4 : angle 0.86820 / 0.46 ( 3) link_NAG-ASN : bond 0.00583 / 0.29 ( 11) link_NAG-ASN : angle 3.34008 / 2.02 ( 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 351 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 286 time to evaluate : 0.721 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 322 MET cc_start: 0.6944 (mmm) cc_final: 0.6175 (mmm) REVERT: A 346 ARG cc_start: 0.5933 (tpm170) cc_final: 0.5425 (ptp-170) REVERT: A 361 LYS cc_start: 0.7302 (mmtt) cc_final: 0.6904 (mttt) REVERT: B 554 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8358 (mtpt) REVERT: C 358 PHE cc_start: 0.8284 (t80) cc_final: 0.7645 (t80) REVERT: D 506 MET cc_start: 0.8449 (mtp) cc_final: 0.8184 (mtm) REVERT: E 419 ASN cc_start: 0.9046 (m110) cc_final: 0.8663 (m110) REVERT: F 551 THR cc_start: 0.8726 (m) cc_final: 0.8477 (t) REVERT: G 455 TYR cc_start: 0.8281 (m-80) cc_final: 0.7532 (m-80) REVERT: G 467 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7680 (mmm-85) REVERT: G 489 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7454 (ptp) REVERT: G 554 LYS cc_start: 0.7711 (mppt) cc_final: 0.7159 (mttt) REVERT: H 370 THR cc_start: -0.0269 (OUTLIER) cc_final: -0.0711 (p) REVERT: H 375 TYR cc_start: 0.4545 (t80) cc_final: 0.4269 (t80) REVERT: H 468 GLU cc_start: 0.8220 (tt0) cc_final: 0.7953 (tp30) REVERT: H 491 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8138 (mtt-85) REVERT: H 529 ASN cc_start: 0.8266 (m-40) cc_final: 0.7709 (m-40) REVERT: K 529 ASN cc_start: 0.8428 (m-40) cc_final: 0.8185 (m-40) REVERT: K 553 ASP cc_start: 0.7908 (t0) cc_final: 0.7676 (t0) REVERT: L 487 GLN cc_start: 0.6164 (mt0) cc_final: 0.5732 (mm110) REVERT: L 515 TYR cc_start: 0.7673 (m-80) cc_final: 0.6932 (m-80) REVERT: L 519 SER cc_start: 0.8362 (m) cc_final: 0.7456 (t) REVERT: J 51 ASP cc_start: 0.7892 (t70) cc_final: 0.7530 (t0) REVERT: J 117 TYR cc_start: 0.6524 (t80) cc_final: 0.6198 (t80) outliers start: 65 outliers final: 44 residues processed: 336 average time/residue: 0.1625 time to fit residues: 81.7782 Evaluate side-chains 315 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 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 554 LYS 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 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 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain F residue 567 VAL 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 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 501 VAL 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 396 ILE 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 522 THR 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: 2.9990 chunk 46 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 211 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** L 518 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.191884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136828 restraints weight = 30950.099| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.29 r_work: 0.3564 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21330 Z= 0.168 Angle : 0.576 11.716 29179 Z= 0.295 Chirality : 0.046 0.445 3415 Planarity : 0.004 0.073 3712 Dihedral : 4.078 32.202 2823 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.43 % Allowed : 16.67 % Favored : 79.91 % 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 are not related in a simple way. whole: -0.40 (0.16), residues: 2592 helix: 0.45 (0.24), residues: 490 sheet: -0.24 (0.18), residues: 744 loop : -0.45 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 491 TYR 0.026 0.001 TYR L 455 PHE 0.035 0.002 PHE F 405 TRP 0.024 0.001 TRP F 382 HIS 0.013 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (21291) covalent geometry : angle 0.56544 / 0.29 (29089) SS BOND : bond 0.00286 / 0.17 ( 27) SS BOND : angle 0.65099 / 0.41 ( 54) hydrogen bonds : bond 0.03414 / 2.19 ( 598) hydrogen bonds : angle 5.28135 / 3.87 ( 1842) link_BETA1-4 : bond 0.00631 / 0.33 ( 1) link_BETA1-4 : angle 0.92191 / 0.49 ( 3) link_NAG-ASN : bond 0.00541 / 0.26 ( 11) link_NAG-ASN : angle 3.29107 / 1.98 ( 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 360 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 279 time to evaluate : 0.812 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 322 MET cc_start: 0.7103 (mmm) cc_final: 0.6762 (mmm) REVERT: M 340 ILE cc_start: 0.6610 (tp) cc_final: 0.6352 (tp) REVERT: A 361 LYS cc_start: 0.7327 (mmtt) cc_final: 0.7002 (mttt) REVERT: A 570 ASP cc_start: 0.8153 (t0) cc_final: 0.7879 (t0) REVERT: B 419 ASN cc_start: 0.8645 (m110) cc_final: 0.8309 (p0) REVERT: B 570 ASP cc_start: 0.6435 (m-30) cc_final: 0.5739 (t0) REVERT: C 358 PHE cc_start: 0.8375 (t80) cc_final: 0.7787 (t80) REVERT: D 506 MET cc_start: 0.8433 (mtp) cc_final: 0.8200 (mtm) REVERT: E 419 ASN cc_start: 0.8995 (m110) cc_final: 0.8587 (m110) REVERT: E 568 MET cc_start: 0.6207 (tpt) cc_final: 0.5934 (tpp) REVERT: F 551 THR cc_start: 0.8761 (m) cc_final: 0.8520 (t) REVERT: G 455 TYR cc_start: 0.8354 (m-80) cc_final: 0.7655 (m-80) REVERT: G 467 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7567 (mmm-85) REVERT: G 489 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7482 (ptp) REVERT: G 554 LYS cc_start: 0.7811 (mppt) cc_final: 0.7288 (mttt) REVERT: H 370 THR cc_start: -0.0193 (OUTLIER) cc_final: -0.0618 (p) REVERT: H 375 TYR cc_start: 0.4602 (t80) cc_final: 0.4292 (t80) REVERT: H 468 GLU cc_start: 0.8213 (tt0) cc_final: 0.7989 (tp30) REVERT: H 529 ASN cc_start: 0.8206 (m-40) cc_final: 0.7681 (m-40) REVERT: K 483 ASP cc_start: 0.7641 (t70) cc_final: 0.7199 (t0) REVERT: K 518 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7585 (m-70) REVERT: K 553 ASP cc_start: 0.8037 (t0) cc_final: 0.7710 (t0) REVERT: K 554 LYS cc_start: 0.8377 (tttt) cc_final: 0.8126 (tttt) REVERT: L 515 TYR cc_start: 0.7636 (m-80) cc_final: 0.6872 (m-80) REVERT: L 519 SER cc_start: 0.8433 (m) cc_final: 0.7491 (t) REVERT: J 41 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8764 (m) REVERT: J 51 ASP cc_start: 0.8182 (t70) cc_final: 0.7974 (t0) REVERT: J 117 TYR cc_start: 0.6709 (t80) cc_final: 0.6425 (t80) outliers start: 81 outliers final: 61 residues processed: 343 average time/residue: 0.1572 time to fit residues: 81.5993 Evaluate side-chains 330 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 465 ASN 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 C residue 522 THR Chi-restraints excluded: chain C residue 552 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 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 369 VAL 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 F residue 476 VAL Chi-restraints excluded: chain F residue 567 VAL 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 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 518 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 212 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 490 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 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 = 0.4427 r_free = 0.4427 target = 0.191453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136157 restraints weight = 31705.252| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.60 r_work: 0.3504 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21330 Z= 0.195 Angle : 0.594 11.953 29179 Z= 0.305 Chirality : 0.047 0.452 3415 Planarity : 0.004 0.078 3712 Dihedral : 4.191 35.853 2823 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.51 % Allowed : 16.92 % Favored : 79.57 % 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 are not related in a simple way. whole: -0.49 (0.16), residues: 2592 helix: 0.41 (0.23), residues: 489 sheet: -0.36 (0.18), residues: 749 loop : -0.48 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 491 TYR 0.027 0.001 TYR L 455 PHE 0.028 0.002 PHE F 405 TRP 0.025 0.001 TRP F 382 HIS 0.009 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (21291) covalent geometry : angle 0.58206 / 0.30 (29089) SS BOND : bond 0.00326 / 0.20 ( 27) SS BOND : angle 0.67193 / 0.44 ( 54) hydrogen bonds : bond 0.03494 / 2.25 ( 598) hydrogen bonds : angle 5.34047 / 3.92 ( 1842) link_BETA1-4 : bond 0.00621 / 0.33 ( 1) link_BETA1-4 : angle 0.89026 / 0.48 ( 3) link_NAG-ASN : bond 0.00637 / 0.31 ( 11) link_NAG-ASN : angle 3.48052 / 2.03 ( 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 371 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 288 time to evaluate : 0.727 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 300 ASN cc_start: 0.8415 (t0) cc_final: 0.8073 (t0) REVERT: M 322 MET cc_start: 0.7139 (mmm) cc_final: 0.6850 (mmm) REVERT: M 340 ILE cc_start: 0.6739 (tp) cc_final: 0.6480 (tp) REVERT: A 361 LYS cc_start: 0.7413 (mmtt) cc_final: 0.7057 (mttt) REVERT: A 570 ASP cc_start: 0.8288 (t0) cc_final: 0.7914 (t0) REVERT: B 419 ASN cc_start: 0.8603 (m110) cc_final: 0.8250 (p0) REVERT: D 506 MET cc_start: 0.8529 (mtp) cc_final: 0.8319 (mtm) REVERT: E 419 ASN cc_start: 0.9004 (m110) cc_final: 0.8592 (m110) REVERT: E 568 MET cc_start: 0.6345 (tpt) cc_final: 0.6077 (tpp) REVERT: F 551 THR cc_start: 0.8851 (m) cc_final: 0.8631 (t) REVERT: G 489 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7483 (ptp) REVERT: G 554 LYS cc_start: 0.7895 (mppt) cc_final: 0.7399 (mtpt) REVERT: H 370 THR cc_start: -0.0161 (OUTLIER) cc_final: -0.0576 (p) REVERT: H 468 GLU cc_start: 0.8258 (tt0) cc_final: 0.8003 (tp30) REVERT: H 529 ASN cc_start: 0.8298 (m-40) cc_final: 0.7866 (m-40) REVERT: K 483 ASP cc_start: 0.7775 (t70) cc_final: 0.7575 (t0) REVERT: K 553 ASP cc_start: 0.8176 (t0) cc_final: 0.7856 (t0) REVERT: K 554 LYS cc_start: 0.8549 (tttt) cc_final: 0.8090 (tttm) REVERT: L 515 TYR cc_start: 0.7660 (m-80) cc_final: 0.6840 (m-80) REVERT: L 534 TYR cc_start: 0.7443 (m-80) cc_final: 0.7171 (m-80) REVERT: L 553 ASP cc_start: 0.6920 (m-30) cc_final: 0.6702 (m-30) REVERT: J 51 ASP cc_start: 0.8462 (t70) cc_final: 0.8261 (t0) REVERT: J 117 TYR cc_start: 0.6917 (t80) cc_final: 0.6598 (t80) outliers start: 83 outliers final: 70 residues processed: 351 average time/residue: 0.1563 time to fit residues: 82.4997 Evaluate side-chains 348 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 402 ASN 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 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 465 ASN 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 C residue 522 THR Chi-restraints excluded: chain C residue 552 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 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL 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 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 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 483 ASP Chi-restraints excluded: chain H residue 484 VAL 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 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 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 Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN 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: 0.8980 chunk 90 optimal weight: 0.0070 chunk 135 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 0.0770 chunk 220 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS C 400 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** 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 = 0.4439 r_free = 0.4439 target = 0.193019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.138199 restraints weight = 31503.338| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.45 r_work: 0.3548 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4284 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= 0.121 Angle : 0.563 11.246 29179 Z= 0.288 Chirality : 0.046 0.429 3415 Planarity : 0.004 0.078 3712 Dihedral : 4.084 34.254 2823 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.43 % Allowed : 17.77 % Favored : 78.81 % 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 are not related in a simple way. whole: -0.40 (0.16), residues: 2592 helix: 0.47 (0.24), residues: 490 sheet: -0.24 (0.19), residues: 728 loop : -0.45 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 491 TYR 0.037 0.001 TYR L 455 PHE 0.028 0.001 PHE F 405 TRP 0.026 0.001 TRP F 382 HIS 0.006 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (21291) covalent geometry : angle 0.55214 / 0.29 (29089) SS BOND : bond 0.00203 / 0.13 ( 27) SS BOND : angle 0.51216 / 0.34 ( 54) hydrogen bonds : bond 0.03192 / 2.04 ( 598) hydrogen bonds : angle 5.13567 / 3.78 ( 1842) link_BETA1-4 : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : angle 1.30889 / 0.69 ( 3) link_NAG-ASN : bond 0.00661 / 0.40 ( 11) link_NAG-ASN : angle 3.37781 / 1.99 ( 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 363 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 282 time to evaluate : 0.722 Fit side-chains 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 322 MET cc_start: 0.7071 (mmm) cc_final: 0.6739 (mmm) REVERT: M 340 ILE cc_start: 0.6528 (tp) cc_final: 0.6261 (tp) REVERT: A 361 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6983 (mttt) REVERT: A 499 LYS cc_start: 0.9216 (tttm) cc_final: 0.8959 (tttm) REVERT: A 570 ASP cc_start: 0.8190 (t0) cc_final: 0.7802 (t0) REVERT: B 419 ASN cc_start: 0.8628 (m110) cc_final: 0.8272 (p0) REVERT: B 451 ARG cc_start: 0.8662 (ptm-80) cc_final: 0.8322 (ptp90) REVERT: C 358 PHE cc_start: 0.8347 (t80) cc_final: 0.7763 (t80) REVERT: D 506 MET cc_start: 0.8483 (mtp) cc_final: 0.8235 (mtm) REVERT: E 419 ASN cc_start: 0.8966 (m110) cc_final: 0.8537 (m110) REVERT: E 553 ASP cc_start: 0.7566 (m-30) cc_final: 0.7318 (m-30) REVERT: E 568 MET cc_start: 0.6271 (tpt) cc_final: 0.6009 (tpp) REVERT: F 551 THR cc_start: 0.8747 (m) cc_final: 0.8526 (t) REVERT: G 455 TYR cc_start: 0.8248 (m-80) cc_final: 0.7488 (m-80) REVERT: G 489 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7470 (ptp) REVERT: G 554 LYS cc_start: 0.7820 (mppt) cc_final: 0.7372 (mtpt) REVERT: H 370 THR cc_start: -0.0254 (OUTLIER) cc_final: -0.0696 (p) REVERT: H 468 GLU cc_start: 0.8280 (tt0) cc_final: 0.8019 (tp30) REVERT: H 520 ILE cc_start: 0.9090 (mt) cc_final: 0.8887 (tt) REVERT: H 529 ASN cc_start: 0.8298 (m-40) cc_final: 0.7821 (m-40) REVERT: K 483 ASP cc_start: 0.7709 (t70) cc_final: 0.7505 (t0) REVERT: K 553 ASP cc_start: 0.8004 (t0) cc_final: 0.7793 (t0) REVERT: K 554 LYS cc_start: 0.8456 (tttt) cc_final: 0.8233 (tttt) REVERT: L 450 HIS cc_start: 0.6745 (t-90) cc_final: 0.6501 (t-90) REVERT: L 487 GLN cc_start: 0.6254 (mt0) cc_final: 0.5840 (mm110) REVERT: L 515 TYR cc_start: 0.7671 (m-80) cc_final: 0.6871 (m-80) REVERT: L 519 SER cc_start: 0.8467 (m) cc_final: 0.7512 (t) REVERT: L 534 TYR cc_start: 0.7383 (m-80) cc_final: 0.7063 (m-80) REVERT: J 46 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7405 (mmt180) REVERT: J 117 TYR cc_start: 0.6819 (t80) cc_final: 0.6533 (t80) outliers start: 81 outliers final: 64 residues processed: 341 average time/residue: 0.1476 time to fit residues: 76.5076 Evaluate side-chains 333 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 267 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 487 GLN 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 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 465 ASN 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 552 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 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 369 VAL 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 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 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 483 ASP 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 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 L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN F 529 ASN G 493 GLN K 529 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.188009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126263 restraints weight = 31660.579| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.21 r_work: 0.3476 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21330 Z= 0.271 Angle : 0.668 12.083 29179 Z= 0.344 Chirality : 0.049 0.464 3415 Planarity : 0.005 0.080 3712 Dihedral : 4.494 37.941 2823 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.55 % Allowed : 18.02 % Favored : 78.43 % 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 are not related in a simple way. whole: -0.66 (0.16), residues: 2592 helix: 0.27 (0.23), residues: 490 sheet: -0.50 (0.18), residues: 731 loop : -0.57 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 491 TYR 0.046 0.002 TYR M 235 PHE 0.026 0.002 PHE F 405 TRP 0.028 0.002 TRP F 382 HIS 0.014 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.27 (21291) covalent geometry : angle 0.65746 / 0.34 (29089) SS BOND : bond 0.00455 / 0.29 ( 27) SS BOND : angle 0.76414 / 0.51 ( 54) hydrogen bonds : bond 0.03863 / 2.49 ( 598) hydrogen bonds : angle 5.56505 / 4.08 ( 1842) link_BETA1-4 : bond 0.00238 / 0.13 ( 1) link_BETA1-4 : angle 1.01852 / 0.56 ( 3) link_NAG-ASN : bond 0.00590 / 0.26 ( 11) link_NAG-ASN : angle 3.54743 / 2.07 ( 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 365 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 281 time to evaluate : 0.705 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: symmetry clash REVERT: M 300 ASN cc_start: 0.8458 (t0) cc_final: 0.8106 (t0) REVERT: A 361 LYS cc_start: 0.7488 (mmtt) cc_final: 0.7155 (mttt) REVERT: A 396 ILE cc_start: 0.3053 (mm) cc_final: 0.2711 (mp) REVERT: B 570 ASP cc_start: 0.6675 (m-30) cc_final: 0.6263 (t0) REVERT: C 376 ASP cc_start: 0.5065 (m-30) cc_final: 0.4850 (m-30) REVERT: D 568 MET cc_start: 0.7725 (mpp) cc_final: 0.7413 (mpp) REVERT: E 419 ASN cc_start: 0.8996 (m110) cc_final: 0.8563 (m110) REVERT: E 553 ASP cc_start: 0.7702 (m-30) cc_final: 0.7491 (m-30) REVERT: G 468 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: G 489 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7534 (ptp) REVERT: G 554 LYS cc_start: 0.7908 (mppt) cc_final: 0.7517 (mtpt) REVERT: H 370 THR cc_start: -0.0391 (OUTLIER) cc_final: -0.0756 (p) REVERT: H 468 GLU cc_start: 0.8227 (tt0) cc_final: 0.7968 (tp30) REVERT: H 529 ASN cc_start: 0.8296 (m-40) cc_final: 0.7847 (m-40) REVERT: K 419 ASN cc_start: 0.7795 (m-40) cc_final: 0.7591 (m110) REVERT: K 553 ASP cc_start: 0.8218 (t0) cc_final: 0.7968 (t70) REVERT: L 487 GLN cc_start: 0.6307 (mt0) cc_final: 0.5840 (mm110) REVERT: L 515 TYR cc_start: 0.7596 (m-80) cc_final: 0.6599 (m-80) REVERT: L 534 TYR cc_start: 0.7428 (m-80) cc_final: 0.7184 (m-80) REVERT: J 117 TYR cc_start: 0.7149 (t80) cc_final: 0.6857 (t80) outliers start: 84 outliers final: 71 residues processed: 347 average time/residue: 0.1497 time to fit residues: 78.2238 Evaluate side-chains 335 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 261 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 402 ASN 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 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 465 ASN 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 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 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL 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 538 VAL Chi-restraints excluded: chain E residue 554 LYS 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 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 468 GLU Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 493 GLN 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 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 536 CYS 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 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 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 Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 233 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 256 optimal weight: 0.0010 chunk 89 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN K 490 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.191683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136986 restraints weight = 31498.431| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.50 r_work: 0.3518 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21330 Z= 0.141 Angle : 0.602 11.057 29179 Z= 0.309 Chirality : 0.047 0.434 3415 Planarity : 0.005 0.088 3712 Dihedral : 4.362 40.613 2823 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.21 % Allowed : 18.53 % Favored : 78.26 % 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 are not related in a simple way. whole: -0.57 (0.16), residues: 2592 helix: 0.35 (0.24), residues: 489 sheet: -0.41 (0.18), residues: 737 loop : -0.54 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 491 TYR 0.041 0.002 TYR M 235 PHE 0.026 0.002 PHE F 405 TRP 0.034 0.001 TRP F 382 HIS 0.007 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (21291) covalent geometry : angle 0.59117 / 0.31 (29089) SS BOND : bond 0.00240 / 0.15 ( 27) SS BOND : angle 0.57375 / 0.38 ( 54) hydrogen bonds : bond 0.03341 / 2.14 ( 598) hydrogen bonds : angle 5.28591 / 3.89 ( 1842) link_BETA1-4 : bond 0.00576 / 0.30 ( 1) link_BETA1-4 : angle 0.96777 / 0.53 ( 3) link_NAG-ASN : bond 0.00529 / 0.25 ( 11) link_NAG-ASN : angle 3.39868 / 1.99 ( 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 349 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 273 time to evaluate : 0.709 Fit side-chains 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: symmetry clash REVERT: M 300 ASN cc_start: 0.8430 (t0) cc_final: 0.8081 (t0) REVERT: M 340 ILE cc_start: 0.6697 (tp) cc_final: 0.6433 (tp) REVERT: A 361 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7104 (mttt) REVERT: A 391 LYS cc_start: 0.7000 (mptt) cc_final: 0.6783 (tmtt) REVERT: A 396 ILE cc_start: 0.3351 (mm) cc_final: 0.3042 (mp) REVERT: A 499 LYS cc_start: 0.9195 (tttm) cc_final: 0.8934 (ttmt) REVERT: A 545 ASN cc_start: 0.7979 (m-40) cc_final: 0.7617 (t0) REVERT: B 419 ASN cc_start: 0.8551 (m110) cc_final: 0.8169 (p0) REVERT: B 451 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8282 (ptp90) REVERT: E 419 ASN cc_start: 0.8979 (m110) cc_final: 0.8614 (m110) REVERT: E 553 ASP cc_start: 0.7635 (m-30) cc_final: 0.7366 (m-30) REVERT: F 551 THR cc_start: 0.8897 (m) cc_final: 0.8666 (t) REVERT: G 455 TYR cc_start: 0.8255 (m-80) cc_final: 0.7484 (m-80) REVERT: G 468 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: G 489 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7467 (ptp) REVERT: G 526 GLU cc_start: 0.7532 (mp0) cc_final: 0.7230 (mp0) REVERT: G 554 LYS cc_start: 0.7883 (mppt) cc_final: 0.7417 (mtpt) REVERT: H 370 THR cc_start: -0.0135 (OUTLIER) cc_final: -0.0470 (p) REVERT: H 468 GLU cc_start: 0.8322 (tt0) cc_final: 0.8061 (tp30) REVERT: H 529 ASN cc_start: 0.8306 (m-40) cc_final: 0.7846 (m-40) REVERT: K 498 GLU cc_start: 0.7998 (mp0) cc_final: 0.7641 (mp0) REVERT: K 553 ASP cc_start: 0.8191 (t0) cc_final: 0.7825 (t70) REVERT: L 487 GLN cc_start: 0.6022 (mt0) cc_final: 0.5608 (mm110) REVERT: L 515 TYR cc_start: 0.7578 (m-80) cc_final: 0.6697 (m-80) REVERT: L 519 SER cc_start: 0.8390 (m) cc_final: 0.7412 (t) REVERT: L 534 TYR cc_start: 0.7377 (m-80) cc_final: 0.7085 (m-80) REVERT: J 47 GLU cc_start: 0.8214 (mp0) cc_final: 0.7387 (mp0) REVERT: J 117 TYR cc_start: 0.6963 (t80) cc_final: 0.6560 (t80) REVERT: J 125 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7734 (tt0) outliers start: 76 outliers final: 67 residues processed: 331 average time/residue: 0.1457 time to fit residues: 72.5860 Evaluate side-chains 339 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 402 ASN 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 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 465 ASN 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 552 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 547 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL 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 413 ILE Chi-restraints excluded: chain E residue 554 LYS 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 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 468 GLU 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 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 536 CYS 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 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 524 SER Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 193 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.190906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135537 restraints weight = 31567.084| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.61 r_work: 0.3497 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4775 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= 0.163 Angle : 0.597 11.401 29179 Z= 0.305 Chirality : 0.046 0.446 3415 Planarity : 0.005 0.084 3712 Dihedral : 4.302 39.143 2823 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.21 % Allowed : 18.65 % Favored : 78.13 % 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 are not related in a simple way. whole: -0.60 (0.16), residues: 2592 helix: 0.39 (0.24), residues: 490 sheet: -0.44 (0.18), residues: 744 loop : -0.57 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 491 TYR 0.042 0.002 TYR M 235 PHE 0.025 0.002 PHE F 405 TRP 0.030 0.001 TRP F 382 HIS 0.009 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (21291) covalent geometry : angle 0.58620 / 0.30 (29089) SS BOND : bond 0.00300 / 0.20 ( 27) SS BOND : angle 0.53841 / 0.35 ( 54) hydrogen bonds : bond 0.03346 / 2.13 ( 598) hydrogen bonds : angle 5.29970 / 3.90 ( 1842) link_BETA1-4 : bond 0.00603 / 0.32 ( 1) link_BETA1-4 : angle 0.96540 / 0.53 ( 3) link_NAG-ASN : bond 0.00536 / 0.24 ( 11) link_NAG-ASN : angle 3.37496 / 1.97 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.59 seconds wall clock time: 94 minutes 17.49 seconds (5657.49 seconds total)