Starting phenix.real_space_refine on Thu Jun 19 16:18:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg2_33805/06_2025/7yg2_33805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg2_33805/06_2025/7yg2_33805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yg2_33805/06_2025/7yg2_33805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg2_33805/06_2025/7yg2_33805.map" model { file = "/net/cci-nas-00/data/ceres_data/7yg2_33805/06_2025/7yg2_33805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg2_33805/06_2025/7yg2_33805.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 23 Chain: "M" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2257 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1761 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 18, 'TRANS': 208} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.30, per 1000 atoms: 0.69 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: 4.80 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.95 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: 7.18 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6747 1.34 - 1.46: 4867 1.46 - 1.58: 9534 1.58 - 1.70: 1 1.70 - 1.82: 142 Bond restraints: 21291 Sorted by residual: bond pdb=" C1 NAG G 601 " pdb=" O5 NAG G 601 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" C1 NAG H 601 " pdb=" O5 NAG H 601 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" CB PRO D 497 " pdb=" CG PRO D 497 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.45e+00 ... (remaining 21286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 28337 1.68 - 3.37: 637 3.37 - 5.05: 80 5.05 - 6.74: 30 6.74 - 8.42: 5 Bond angle restraints: 29089 Sorted by residual: angle pdb=" CA PRO D 497 " pdb=" N PRO D 497 " pdb=" CD PRO D 497 " ideal model delta sigma weight residual 112.00 105.15 6.85 1.40e+00 5.10e-01 2.40e+01 angle pdb=" N GLY A 531 " pdb=" CA GLY A 531 " pdb=" C GLY A 531 " ideal model delta sigma weight residual 111.36 116.91 -5.55 1.17e+00 7.31e-01 2.25e+01 angle pdb=" CA PRO E 497 " pdb=" N PRO E 497 " pdb=" CD PRO E 497 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C THR E 370 " pdb=" N ASP E 371 " pdb=" CA ASP E 371 " ideal model delta sigma weight residual 122.46 127.95 -5.49 1.41e+00 5.03e-01 1.51e+01 angle pdb=" C THR A 530 " pdb=" N GLY A 531 " pdb=" CA GLY A 531 " ideal model delta sigma weight residual 119.92 123.57 -3.65 9.60e-01 1.09e+00 1.45e+01 ... (remaining 29084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 12208 23.03 - 46.06: 798 46.06 - 69.08: 56 69.08 - 92.11: 34 92.11 - 115.14: 21 Dihedral angle restraints: 13117 sinusoidal: 5369 harmonic: 7748 Sorted by residual: dihedral pdb=" CB CYS D 367 " pdb=" SG CYS D 367 " pdb=" SG CYS D 426 " pdb=" CB CYS D 426 " ideal model delta sinusoidal sigma weight residual 93.00 162.63 -69.63 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS L 575 " pdb=" SG CYS L 575 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS F 367 " pdb=" SG CYS F 367 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual 93.00 34.82 58.18 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 13114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3092 0.085 - 0.170: 318 0.170 - 0.256: 4 0.256 - 0.341: 0 0.341 - 0.426: 1 Chirality restraints: 3415 Sorted by residual: chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL H 390 " pdb=" CA VAL H 390 " pdb=" CG1 VAL H 390 " pdb=" CG2 VAL H 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1 NAG G 601 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG G 601 " pdb=" O5 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3412 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 496 " 0.093 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO E 497 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO E 497 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO E 497 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 496 " -0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO D 497 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO D 497 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 497 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 457 " -0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 458 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " -0.050 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1199 2.74 - 3.28: 20363 3.28 - 3.82: 33211 3.82 - 4.36: 38461 4.36 - 4.90: 66350 Nonbonded interactions: 159584 Sorted by model distance: nonbonded pdb=" O MET L 489 " pdb=" OG1 THR L 535 " model vdw 2.196 3.040 nonbonded pdb=" O ALA H 448 " pdb=" OG SER H 480 " model vdw 2.228 3.040 nonbonded pdb=" O ILE B 350 " pdb=" OG1 THR B 366 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASN L 563 " pdb=" ND2 ASN J 36 " model vdw 2.295 3.120 nonbonded pdb=" OG1 THR B 383 " pdb=" OG1 THR B 425 " model vdw 2.295 3.040 ... (remaining 159579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 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 568 or res \ id 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 568 or res \ id 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 568 or resid 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 568 or res \ id 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.040 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 49.200 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 21330 Z= 0.138 Angle : 0.625 14.350 29179 Z= 0.319 Chirality : 0.046 0.426 3415 Planarity : 0.006 0.138 3712 Dihedral : 15.078 115.141 7978 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.001 TRP D 418 HIS 0.009 0.001 HIS K 430 PHE 0.029 0.002 PHE C 348 TYR 0.023 0.001 TYR B 500 ARG 0.014 0.001 ARG C 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 11) link_NAG-ASN : angle 4.18640 ( 33) link_BETA1-4 : bond 0.01421 ( 1) link_BETA1-4 : angle 1.14811 ( 3) hydrogen bonds : bond 0.23920 ( 598) hydrogen bonds : angle 9.24349 ( 1842) SS BOND : bond 0.00216 ( 27) SS BOND : angle 0.85500 ( 54) covalent geometry : bond 0.00292 (21291) covalent geometry : angle 0.60835 (29089) *********************** 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 : 2.423 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 270 ILE cc_start: 0.7017 (mt) cc_final: 0.6814 (mt) REVERT: M 332 ASN cc_start: 0.6987 (t0) cc_final: 0.6765 (t0) REVERT: M 340 ILE cc_start: 0.7267 (tp) cc_final: 0.7052 (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: 0.7196 (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: 0.5498 (p0) REVERT: K 529 ASN cc_start: 0.7985 (m-40) cc_final: 0.7677 (m110) REVERT: L 451 ARG cc_start: 0.7639 (ptm-80) cc_final: 0.7396 (ttp-110) REVERT: L 461 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6864 (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: 0.7358 (m-40) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3489 time to fit residues: 207.4413 Evaluate side-chains 297 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 ASN A 400 HIS A 529 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 545 ASN K 400 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.195458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137454 restraints weight = 31917.920| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.57 r_work: 0.3587 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 21330 Z= 0.298 Angle : 0.735 13.868 29179 Z= 0.380 Chirality : 0.051 0.466 3415 Planarity : 0.006 0.074 3712 Dihedral : 8.681 110.321 3075 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 11.34 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2592 helix: -0.15 (0.22), residues: 487 sheet: -0.16 (0.19), residues: 743 loop : -0.58 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 382 HIS 0.013 0.002 HIS E 518 PHE 0.025 0.003 PHE A 479 TYR 0.026 0.002 TYR M 337 ARG 0.006 0.001 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 11) link_NAG-ASN : angle 3.98012 ( 33) link_BETA1-4 : bond 0.02590 ( 1) link_BETA1-4 : angle 3.09784 ( 3) hydrogen bonds : bond 0.04718 ( 598) hydrogen bonds : angle 6.03593 ( 1842) SS BOND : bond 0.00637 ( 27) SS BOND : angle 1.06560 ( 54) covalent geometry : bond 0.00692 (21291) covalent geometry : angle 0.72152 (29089) *********************** 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 369 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 2.346 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 235 TYR cc_start: 0.7970 (m-80) cc_final: 0.7743 (m-80) REVERT: M 337 TYR cc_start: 0.7005 (p90) cc_final: 0.6787 (p90) REVERT: M 418 TYR cc_start: 0.7730 (t80) cc_final: 0.7523 (t80) REVERT: A 570 ASP cc_start: 0.7999 (t70) cc_final: 0.7730 (t0) REVERT: B 419 ASN cc_start: 0.8684 (m110) cc_final: 0.8349 (p0) REVERT: C 495 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8394 (mt) REVERT: C 506 MET cc_start: 0.8685 (mtm) cc_final: 0.8252 (mtp) REVERT: D 506 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: E 419 ASN cc_start: 0.8967 (m110) cc_final: 0.8640 (m110) REVERT: F 529 ASN cc_start: 0.7642 (m110) cc_final: 0.6959 (m-40) REVERT: G 455 TYR cc_start: 0.8353 (m-80) cc_final: 0.7706 (m-80) REVERT: G 467 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7399 (mmm-85) REVERT: G 506 MET cc_start: 0.8315 (pmm) cc_final: 0.8021 (pmm) REVERT: G 554 LYS cc_start: 0.7514 (mppt) cc_final: 0.6929 (mttt) REVERT: H 375 TYR cc_start: 0.4197 (t80) cc_final: 0.3933 (t80) REVERT: H 468 GLU cc_start: 0.8108 (tt0) cc_final: 0.7819 (tm-30) REVERT: H 529 ASN cc_start: 0.7916 (m-40) cc_final: 0.7524 (m-40) REVERT: K 414 CYS cc_start: 0.8162 (t) cc_final: 0.7432 (m) REVERT: K 529 ASN cc_start: 0.8461 (m-40) cc_final: 0.8178 (m110) REVERT: K 553 ASP cc_start: 0.7811 (t0) cc_final: 0.7434 (t70) REVERT: L 461 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7477 (mmm-85) REVERT: L 515 TYR cc_start: 0.7793 (m-80) cc_final: 0.7124 (m-80) REVERT: J 51 ASP cc_start: 0.7259 (t70) cc_final: 0.6947 (t0) REVERT: J 117 TYR cc_start: 0.6548 (t80) cc_final: 0.6284 (t80) outliers start: 48 outliers final: 31 residues processed: 350 average time/residue: 0.3726 time to fit residues: 193.8434 Evaluate side-chains 304 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 2.445 ------------------------------------------------------------------------------- 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 501 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 547 VAL 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 400 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 98 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 233 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 402 ASN A 529 ASN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN C 493 GLN D 385 GLN D 545 ASN E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN G 400 HIS G 529 ASN H 545 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** ** 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 = 0.4482 r_free = 0.4482 target = 0.197081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.143888 restraints weight = 31798.313| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.56 r_work: 0.3613 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21330 Z= 0.137 Angle : 0.574 12.299 29179 Z= 0.293 Chirality : 0.046 0.456 3415 Planarity : 0.004 0.072 3712 Dihedral : 7.738 104.176 3075 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 13.41 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2592 helix: 0.16 (0.23), residues: 487 sheet: -0.15 (0.19), residues: 727 loop : -0.47 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 382 HIS 0.008 0.001 HIS K 430 PHE 0.022 0.002 PHE E 354 TYR 0.029 0.001 TYR L 455 ARG 0.010 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 11) link_NAG-ASN : angle 3.59003 ( 33) link_BETA1-4 : bond 0.00715 ( 1) link_BETA1-4 : angle 2.84840 ( 3) hydrogen bonds : bond 0.03813 ( 598) hydrogen bonds : angle 5.60501 ( 1842) SS BOND : bond 0.00232 ( 27) SS BOND : angle 0.65029 ( 54) covalent geometry : bond 0.00307 (21291) covalent geometry : angle 0.56101 (29089) *********************** 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 335 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.7980 (m-80) cc_final: 0.7745 (m-80) REVERT: A 570 ASP cc_start: 0.7902 (t70) cc_final: 0.7671 (t0) REVERT: C 495 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8469 (mt) REVERT: D 506 MET cc_start: 0.8608 (mtp) cc_final: 0.8357 (mtm) REVERT: E 419 ASN cc_start: 0.9003 (m110) cc_final: 0.8639 (m110) REVERT: G 455 TYR cc_start: 0.8283 (m-80) cc_final: 0.7584 (m-80) REVERT: G 489 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7504 (ptp) REVERT: G 554 LYS cc_start: 0.7536 (mppt) cc_final: 0.7003 (mttt) REVERT: H 375 TYR cc_start: 0.4418 (t80) cc_final: 0.4164 (t80) REVERT: H 468 GLU cc_start: 0.8058 (tt0) cc_final: 0.7857 (tp30) REVERT: H 529 ASN cc_start: 0.7999 (m-40) cc_final: 0.7436 (m-40) REVERT: K 410 GLU cc_start: 0.5653 (tm-30) cc_final: 0.5369 (tm-30) REVERT: K 414 CYS cc_start: 0.8104 (t) cc_final: 0.7394 (m) REVERT: K 461 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7192 (mtm-85) REVERT: K 529 ASN cc_start: 0.8436 (m-40) cc_final: 0.8171 (m110) REVERT: K 553 ASP cc_start: 0.7694 (t0) cc_final: 0.7325 (t70) REVERT: L 461 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7412 (mmm-85) REVERT: L 471 THR cc_start: 0.8657 (m) cc_final: 0.8329 (t) REVERT: L 515 TYR cc_start: 0.7707 (m-80) cc_final: 0.7037 (m-80) REVERT: L 519 SER cc_start: 0.8271 (m) cc_final: 0.7372 (t) REVERT: J 51 ASP cc_start: 0.7394 (t70) cc_final: 0.7192 (t0) REVERT: J 117 TYR cc_start: 0.6346 (t80) cc_final: 0.6098 (t80) outliers start: 48 outliers final: 36 residues processed: 323 average time/residue: 0.3613 time to fit residues: 174.8199 Evaluate side-chains 302 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 551 THR 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 501 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 538 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 48 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 161 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN A 393 HIS A 490 GLN A 529 ASN B 419 ASN B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 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 400 HIS F 439 GLN F 463 GLN F 487 GLN F 529 ASN H 545 ASN K 419 ASN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.191069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131725 restraints weight = 32084.960| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.54 r_work: 0.3504 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21330 Z= 0.245 Angle : 0.647 12.554 29179 Z= 0.331 Chirality : 0.048 0.479 3415 Planarity : 0.005 0.070 3712 Dihedral : 7.393 99.785 3075 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.60 % Allowed : 15.10 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2592 helix: 0.19 (0.23), residues: 486 sheet: -0.36 (0.18), residues: 748 loop : -0.58 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 382 HIS 0.014 0.001 HIS A 393 PHE 0.044 0.002 PHE M 346 TYR 0.026 0.002 TYR L 455 ARG 0.009 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 11) link_NAG-ASN : angle 3.61910 ( 33) link_BETA1-4 : bond 0.00627 ( 1) link_BETA1-4 : angle 2.24781 ( 3) hydrogen bonds : bond 0.03926 ( 598) hydrogen bonds : angle 5.65069 ( 1842) SS BOND : bond 0.00395 ( 27) SS BOND : angle 0.71991 ( 54) covalent geometry : bond 0.00576 (21291) covalent geometry : angle 0.63540 (29089) *********************** 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 376 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 291 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8214 (m-80) cc_final: 0.7870 (m-80) REVERT: A 346 ARG cc_start: 0.5900 (tpm170) cc_final: 0.5414 (ptp-170) REVERT: A 361 LYS cc_start: 0.7388 (mmtt) cc_final: 0.6997 (mttt) REVERT: A 570 ASP cc_start: 0.8114 (t70) cc_final: 0.7853 (t0) REVERT: B 419 ASN cc_start: 0.8535 (m110) cc_final: 0.8201 (p0) REVERT: B 570 ASP cc_start: 0.6419 (m-30) cc_final: 0.5623 (t0) REVERT: C 467 ARG cc_start: 0.7591 (mmt180) cc_final: 0.7296 (mmt180) REVERT: C 495 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8699 (mt) REVERT: D 506 MET cc_start: 0.8591 (mtp) cc_final: 0.8383 (mtm) REVERT: E 419 ASN cc_start: 0.9067 (m110) cc_final: 0.8698 (m110) REVERT: G 467 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7575 (mmm-85) REVERT: G 554 LYS cc_start: 0.7887 (mppt) cc_final: 0.7493 (mtpt) REVERT: H 375 TYR cc_start: 0.4608 (t80) cc_final: 0.4323 (t80) REVERT: H 468 GLU cc_start: 0.8238 (tt0) cc_final: 0.7953 (tp30) REVERT: H 529 ASN cc_start: 0.8168 (m-40) cc_final: 0.7568 (m110) REVERT: K 529 ASN cc_start: 0.8424 (m-40) cc_final: 0.8213 (m-40) REVERT: K 554 LYS cc_start: 0.8494 (tttt) cc_final: 0.8276 (tttt) REVERT: L 515 TYR cc_start: 0.7696 (m-80) cc_final: 0.6944 (m-80) REVERT: J 51 ASP cc_start: 0.8215 (t70) cc_final: 0.7956 (t0) REVERT: J 117 TYR cc_start: 0.6883 (t80) cc_final: 0.6635 (t80) outliers start: 85 outliers final: 59 residues processed: 359 average time/residue: 0.3686 time to fit residues: 196.2146 Evaluate side-chains 335 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 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 B residue 541 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 552 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 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 370 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 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 Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 400 HIS A 402 ASN A 529 ASN B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** 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 463 GLN K 400 HIS ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 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 = 0.4427 r_free = 0.4427 target = 0.191755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136159 restraints weight = 31166.380| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.61 r_work: 0.3559 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21330 Z= 0.137 Angle : 0.576 11.851 29179 Z= 0.292 Chirality : 0.046 0.451 3415 Planarity : 0.004 0.077 3712 Dihedral : 7.005 100.634 3075 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 16.62 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2592 helix: 0.35 (0.23), residues: 491 sheet: -0.29 (0.18), residues: 740 loop : -0.51 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 382 HIS 0.009 0.001 HIS L 518 PHE 0.026 0.001 PHE M 346 TYR 0.020 0.001 TYR L 455 ARG 0.010 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 11) link_NAG-ASN : angle 3.62493 ( 33) link_BETA1-4 : bond 0.01041 ( 1) link_BETA1-4 : angle 2.38857 ( 3) hydrogen bonds : bond 0.03363 ( 598) hydrogen bonds : angle 5.33387 ( 1842) SS BOND : bond 0.00222 ( 27) SS BOND : angle 0.58519 ( 54) covalent geometry : bond 0.00316 (21291) covalent geometry : angle 0.56298 (29089) *********************** 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 356 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 2.170 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: symmetry clash REVERT: M 235 TYR cc_start: 0.8187 (m-10) cc_final: 0.7927 (m-80) REVERT: A 361 LYS cc_start: 0.7336 (mmtt) cc_final: 0.7012 (mttt) REVERT: B 554 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8580 (mtpt) REVERT: B 570 ASP cc_start: 0.6384 (m-30) cc_final: 0.5679 (t0) REVERT: D 506 MET cc_start: 0.8474 (mtp) cc_final: 0.8234 (mtm) REVERT: E 419 ASN cc_start: 0.9051 (m110) cc_final: 0.8669 (m110) REVERT: E 554 LYS cc_start: 0.7526 (mtpt) cc_final: 0.7253 (mtpt) REVERT: E 568 MET cc_start: 0.6186 (tpt) cc_final: 0.5889 (tpp) REVERT: F 551 THR cc_start: 0.8770 (m) cc_final: 0.8546 (t) REVERT: G 364 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7049 (tppt) REVERT: G 414 CYS cc_start: 0.6743 (OUTLIER) cc_final: 0.5813 (t) REVERT: G 455 TYR cc_start: 0.8355 (m-80) cc_final: 0.7663 (m-80) REVERT: G 467 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7595 (mmm-85) REVERT: G 489 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7504 (ptp) REVERT: G 554 LYS cc_start: 0.7806 (mppt) cc_final: 0.7278 (mttt) REVERT: H 375 TYR cc_start: 0.4571 (t80) cc_final: 0.4271 (t80) REVERT: H 468 GLU cc_start: 0.8216 (tt0) cc_final: 0.7981 (tp30) REVERT: H 529 ASN cc_start: 0.8273 (m-40) cc_final: 0.7693 (m110) REVERT: K 529 ASN cc_start: 0.8377 (m-40) cc_final: 0.8150 (m-40) REVERT: L 515 TYR cc_start: 0.7643 (m-80) cc_final: 0.6907 (m-80) REVERT: L 519 SER cc_start: 0.8357 (m) cc_final: 0.7456 (t) REVERT: J 51 ASP cc_start: 0.8162 (t70) cc_final: 0.7946 (t0) REVERT: J 117 TYR cc_start: 0.6683 (t80) cc_final: 0.6345 (t80) outliers start: 70 outliers final: 50 residues processed: 342 average time/residue: 0.3790 time to fit residues: 191.6017 Evaluate side-chains 324 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain 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 476 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 414 CYS Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 165 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 400 HIS A 529 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN C 465 ASN E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.189004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128641 restraints weight = 31734.586| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.46 r_work: 0.3469 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21330 Z= 0.245 Angle : 0.645 12.388 29179 Z= 0.329 Chirality : 0.048 0.468 3415 Planarity : 0.005 0.076 3712 Dihedral : 7.078 101.105 3075 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.98 % Allowed : 16.54 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2592 helix: 0.26 (0.23), residues: 491 sheet: -0.51 (0.18), residues: 756 loop : -0.58 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 382 HIS 0.011 0.001 HIS D 400 PHE 0.032 0.002 PHE M 346 TYR 0.024 0.002 TYR L 455 ARG 0.012 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 11) link_NAG-ASN : angle 3.71951 ( 33) link_BETA1-4 : bond 0.00863 ( 1) link_BETA1-4 : angle 2.32571 ( 3) hydrogen bonds : bond 0.03813 ( 598) hydrogen bonds : angle 5.56244 ( 1842) SS BOND : bond 0.00408 ( 27) SS BOND : angle 0.76863 ( 54) covalent geometry : bond 0.00577 (21291) covalent geometry : angle 0.63290 (29089) *********************** 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 386 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 292 time to evaluate : 2.294 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: M 235 TYR cc_start: 0.8240 (m-10) cc_final: 0.7951 (m-80) REVERT: A 361 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7155 (mttt) REVERT: A 570 ASP cc_start: 0.8330 (t0) cc_final: 0.8034 (t0) REVERT: B 419 ASN cc_start: 0.8650 (m110) cc_final: 0.8321 (p0) REVERT: B 570 ASP cc_start: 0.6605 (m-30) cc_final: 0.5941 (t0) REVERT: D 506 MET cc_start: 0.8505 (mtp) cc_final: 0.8301 (mtm) REVERT: E 419 ASN cc_start: 0.9033 (m110) cc_final: 0.8629 (m110) REVERT: E 553 ASP cc_start: 0.7940 (m-30) cc_final: 0.7576 (m-30) REVERT: E 568 MET cc_start: 0.6316 (tpt) cc_final: 0.6114 (tpp) REVERT: G 489 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7518 (ptp) REVERT: G 554 LYS cc_start: 0.7976 (mppt) cc_final: 0.7494 (mtpt) REVERT: H 468 GLU cc_start: 0.8258 (tt0) cc_final: 0.7973 (tp30) REVERT: H 529 ASN cc_start: 0.8225 (m-40) cc_final: 0.7743 (m110) REVERT: K 529 ASN cc_start: 0.8380 (m-40) cc_final: 0.8148 (m-40) REVERT: L 487 GLN cc_start: 0.6217 (mt0) cc_final: 0.5889 (mm110) REVERT: L 515 TYR cc_start: 0.7614 (m-80) cc_final: 0.6834 (m-80) REVERT: L 519 SER cc_start: 0.8681 (m) cc_final: 0.7811 (t) REVERT: L 534 TYR cc_start: 0.7441 (m-80) cc_final: 0.7164 (m-80) REVERT: L 553 ASP cc_start: 0.7037 (m-30) cc_final: 0.6756 (m-30) REVERT: J 51 ASP cc_start: 0.8517 (t70) cc_final: 0.8302 (t0) REVERT: J 117 TYR cc_start: 0.7076 (t80) cc_final: 0.6729 (t80) outliers start: 94 outliers final: 73 residues processed: 369 average time/residue: 0.3596 time to fit residues: 196.7939 Evaluate side-chains 344 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 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 541 GLU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 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 538 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL 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 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 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 466 LEU 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 54 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 204 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 203 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 170 optimal weight: 30.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 400 HIS ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS D 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 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 = 0.4381 r_free = 0.4381 target = 0.187006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125792 restraints weight = 31406.322| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.16 r_work: 0.3454 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 21330 Z= 0.294 Angle : 0.694 12.782 29179 Z= 0.355 Chirality : 0.050 0.481 3415 Planarity : 0.005 0.092 3712 Dihedral : 7.206 101.940 3075 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.15 % Allowed : 17.30 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2592 helix: 0.09 (0.23), residues: 491 sheet: -0.80 (0.18), residues: 767 loop : -0.68 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 382 HIS 0.008 0.001 HIS D 400 PHE 0.032 0.002 PHE M 346 TYR 0.044 0.002 TYR L 455 ARG 0.012 0.001 ARG C 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 11) link_NAG-ASN : angle 3.72810 ( 33) link_BETA1-4 : bond 0.00057 ( 1) link_BETA1-4 : angle 2.34124 ( 3) hydrogen bonds : bond 0.03992 ( 598) hydrogen bonds : angle 5.82337 ( 1842) SS BOND : bond 0.00457 ( 27) SS BOND : angle 0.90163 ( 54) covalent geometry : bond 0.00697 (21291) covalent geometry : angle 0.68217 (29089) *********************** 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 378 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8323 (m-10) cc_final: 0.8047 (m-80) REVERT: M 300 ASN cc_start: 0.8460 (t0) cc_final: 0.8119 (t0) REVERT: A 361 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7205 (mttt) REVERT: B 443 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7354 (ttm110) REVERT: B 570 ASP cc_start: 0.6614 (m-30) cc_final: 0.6219 (t0) REVERT: C 376 ASP cc_start: 0.5146 (m-30) cc_final: 0.4900 (m-30) REVERT: C 467 ARG cc_start: 0.7763 (mmt180) cc_final: 0.7506 (mmt180) REVERT: E 419 ASN cc_start: 0.8894 (m110) cc_final: 0.8496 (m110) REVERT: E 553 ASP cc_start: 0.7910 (m-30) cc_final: 0.7583 (m-30) REVERT: G 489 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7487 (ptp) REVERT: G 526 GLU cc_start: 0.7617 (mp0) cc_final: 0.7278 (mp0) REVERT: G 554 LYS cc_start: 0.7944 (mppt) cc_final: 0.7484 (mtpt) REVERT: H 468 GLU cc_start: 0.8260 (tt0) cc_final: 0.7973 (tp30) REVERT: H 529 ASN cc_start: 0.8298 (m-40) cc_final: 0.7809 (m110) REVERT: K 479 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: L 515 TYR cc_start: 0.7486 (m-80) cc_final: 0.6524 (m-80) REVERT: J 46 ARG cc_start: 0.8001 (mmt180) cc_final: 0.7737 (mmt180) REVERT: J 117 TYR cc_start: 0.7318 (t80) cc_final: 0.6906 (t80) outliers start: 98 outliers final: 74 residues processed: 360 average time/residue: 0.3591 time to fit residues: 192.1492 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 : 2.424 ------------------------------------------------------------------------------- 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 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 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 538 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 567 VAL 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 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 456 LEU Chi-restraints excluded: chain H residue 462 GLU 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 522 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 479 PHE 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 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 54 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 184 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 176 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS B 393 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN F 529 ASN ** G 430 HIS ** 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 = 0.4418 r_free = 0.4418 target = 0.190446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130744 restraints weight = 31722.750| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.20 r_work: 0.3523 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21330 Z= 0.141 Angle : 0.606 11.581 29179 Z= 0.309 Chirality : 0.046 0.421 3415 Planarity : 0.005 0.086 3712 Dihedral : 6.704 100.998 3075 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.38 % Allowed : 18.57 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2592 helix: 0.26 (0.23), residues: 489 sheet: -0.58 (0.18), residues: 746 loop : -0.64 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 382 HIS 0.005 0.001 HIS D 400 PHE 0.051 0.002 PHE F 405 TYR 0.026 0.001 TYR L 455 ARG 0.012 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 11) link_NAG-ASN : angle 3.65892 ( 33) link_BETA1-4 : bond 0.00909 ( 1) link_BETA1-4 : angle 2.21376 ( 3) hydrogen bonds : bond 0.03371 ( 598) hydrogen bonds : angle 5.46381 ( 1842) SS BOND : bond 0.00253 ( 27) SS BOND : angle 0.62080 ( 54) covalent geometry : bond 0.00328 (21291) covalent geometry : angle 0.59297 (29089) *********************** 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 368 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 288 time to evaluate : 2.330 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 235 TYR cc_start: 0.8268 (m-10) cc_final: 0.8067 (m-80) REVERT: A 361 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7148 (mttt) REVERT: A 499 LYS cc_start: 0.9233 (tttm) cc_final: 0.8984 (ttmt) REVERT: A 545 ASN cc_start: 0.7948 (m-40) cc_final: 0.7550 (t0) REVERT: A 570 ASP cc_start: 0.8322 (t0) cc_final: 0.8023 (t0) REVERT: B 419 ASN cc_start: 0.8553 (m110) cc_final: 0.8185 (p0) REVERT: B 443 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7291 (ttm110) REVERT: B 451 ARG cc_start: 0.8728 (ptm-80) cc_final: 0.8357 (ptp90) REVERT: C 376 ASP cc_start: 0.5127 (m-30) cc_final: 0.4878 (m-30) REVERT: E 419 ASN cc_start: 0.8997 (m110) cc_final: 0.8620 (m110) REVERT: E 553 ASP cc_start: 0.7969 (m-30) cc_final: 0.7593 (m-30) REVERT: G 455 TYR cc_start: 0.8279 (m-80) cc_final: 0.7481 (m-80) REVERT: G 468 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: G 489 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7410 (ptp) REVERT: G 526 GLU cc_start: 0.7461 (mp0) cc_final: 0.7102 (mp0) REVERT: G 554 LYS cc_start: 0.7881 (mppt) cc_final: 0.7385 (mtpt) REVERT: H 529 ASN cc_start: 0.8308 (m-40) cc_final: 0.7842 (m110) REVERT: K 498 GLU cc_start: 0.7994 (mp0) cc_final: 0.7742 (mp0) REVERT: L 471 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8360 (m) REVERT: L 487 GLN cc_start: 0.6102 (mt0) cc_final: 0.5760 (mm110) REVERT: L 515 TYR cc_start: 0.7469 (m-80) cc_final: 0.6546 (m-80) REVERT: J 47 GLU cc_start: 0.7893 (mp0) cc_final: 0.7255 (mp0) REVERT: J 117 TYR cc_start: 0.7051 (t80) cc_final: 0.6639 (t80) REVERT: J 125 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7619 (tt0) outliers start: 80 outliers final: 65 residues processed: 350 average time/residue: 0.3490 time to fit residues: 182.7969 Evaluate side-chains 345 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 402 ASN Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 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 462 GLU 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 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 473 THR 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 471 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 125 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 226 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS B 393 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.190444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130768 restraints weight = 31559.076| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.18 r_work: 0.3523 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21330 Z= 0.147 Angle : 0.609 13.580 29179 Z= 0.309 Chirality : 0.046 0.430 3415 Planarity : 0.005 0.091 3712 Dihedral : 6.487 100.783 3075 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.30 % Allowed : 18.99 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2592 helix: 0.25 (0.23), residues: 491 sheet: -0.60 (0.18), residues: 752 loop : -0.58 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 382 HIS 0.017 0.001 HIS B 393 PHE 0.035 0.002 PHE F 405 TYR 0.043 0.002 TYR L 455 ARG 0.010 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 11) link_NAG-ASN : angle 3.56457 ( 33) link_BETA1-4 : bond 0.00893 ( 1) link_BETA1-4 : angle 2.38397 ( 3) hydrogen bonds : bond 0.03340 ( 598) hydrogen bonds : angle 5.37732 ( 1842) SS BOND : bond 0.00259 ( 27) SS BOND : angle 0.55884 ( 54) covalent geometry : bond 0.00345 (21291) covalent geometry : angle 0.59723 (29089) *********************** 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 360 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 2.420 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 235 TYR cc_start: 0.8271 (m-10) cc_final: 0.8066 (m-80) REVERT: M 300 ASN cc_start: 0.8450 (t0) cc_final: 0.8097 (t0) REVERT: A 361 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7122 (mttt) REVERT: A 499 LYS cc_start: 0.9230 (tttm) cc_final: 0.8951 (tttm) REVERT: A 545 ASN cc_start: 0.7965 (m-40) cc_final: 0.7385 (t0) REVERT: A 570 ASP cc_start: 0.8300 (t0) cc_final: 0.7973 (t0) REVERT: B 419 ASN cc_start: 0.8546 (m110) cc_final: 0.8180 (p0) REVERT: B 443 ARG cc_start: 0.7573 (ttm110) cc_final: 0.7288 (ttm110) REVERT: B 451 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.8288 (ptp90) REVERT: C 376 ASP cc_start: 0.5148 (m-30) cc_final: 0.4896 (m-30) REVERT: C 568 MET cc_start: 0.8162 (mmt) cc_final: 0.7856 (mmm) REVERT: E 419 ASN cc_start: 0.8999 (m110) cc_final: 0.8616 (m110) REVERT: E 553 ASP cc_start: 0.7998 (m-30) cc_final: 0.7646 (m-30) REVERT: F 551 THR cc_start: 0.8923 (m) cc_final: 0.8722 (t) REVERT: G 455 TYR cc_start: 0.8280 (m-80) cc_final: 0.7460 (m-80) REVERT: G 489 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7423 (ptp) REVERT: G 526 GLU cc_start: 0.7462 (mp0) cc_final: 0.7114 (mp0) REVERT: G 554 LYS cc_start: 0.7813 (mppt) cc_final: 0.7334 (mtpt) REVERT: H 529 ASN cc_start: 0.8321 (m-40) cc_final: 0.7855 (m110) REVERT: K 498 GLU cc_start: 0.7935 (mp0) cc_final: 0.7711 (mp0) REVERT: L 471 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8316 (m) REVERT: L 487 GLN cc_start: 0.6063 (mt0) cc_final: 0.5719 (mm110) REVERT: L 515 TYR cc_start: 0.7440 (m-80) cc_final: 0.6505 (m-80) REVERT: J 47 GLU cc_start: 0.7852 (mp0) cc_final: 0.7255 (mp0) REVERT: J 117 TYR cc_start: 0.7001 (t80) cc_final: 0.6534 (t80) REVERT: J 125 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7360 (tt0) outliers start: 78 outliers final: 64 residues processed: 342 average time/residue: 0.3597 time to fit residues: 185.3386 Evaluate side-chains 342 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 402 ASN Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 522 THR 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 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR 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 473 THR 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 471 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL 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 132 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.191642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136666 restraints weight = 31481.891| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.49 r_work: 0.3523 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21330 Z= 0.133 Angle : 0.601 12.846 29179 Z= 0.304 Chirality : 0.045 0.419 3415 Planarity : 0.005 0.086 3712 Dihedral : 6.181 99.957 3075 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.09 % Allowed : 19.29 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2592 helix: 0.30 (0.23), residues: 490 sheet: -0.46 (0.18), residues: 742 loop : -0.58 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 382 HIS 0.009 0.001 HIS A 393 PHE 0.034 0.002 PHE F 405 TYR 0.037 0.001 TYR L 455 ARG 0.011 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 11) link_NAG-ASN : angle 3.49443 ( 33) link_BETA1-4 : bond 0.01113 ( 1) link_BETA1-4 : angle 2.59519 ( 3) hydrogen bonds : bond 0.03214 ( 598) hydrogen bonds : angle 5.22913 ( 1842) SS BOND : bond 0.00243 ( 27) SS BOND : angle 0.52479 ( 54) covalent geometry : bond 0.00307 (21291) covalent geometry : angle 0.58931 (29089) ********************** 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 354 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 281 time to evaluate : 2.240 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: M 235 TYR cc_start: 0.8262 (m-10) cc_final: 0.8059 (m-80) REVERT: M 300 ASN cc_start: 0.8446 (t0) cc_final: 0.8096 (t0) REVERT: A 361 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7068 (mttt) REVERT: A 499 LYS cc_start: 0.9229 (tttm) cc_final: 0.8958 (tttm) REVERT: A 545 ASN cc_start: 0.7984 (m-40) cc_final: 0.7435 (t0) REVERT: A 570 ASP cc_start: 0.8203 (t0) cc_final: 0.7861 (t0) REVERT: B 419 ASN cc_start: 0.8540 (m110) cc_final: 0.8170 (p0) REVERT: B 443 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7338 (ttm110) REVERT: B 451 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8284 (ptp90) REVERT: C 376 ASP cc_start: 0.5134 (m-30) cc_final: 0.4917 (m-30) REVERT: C 568 MET cc_start: 0.8150 (mmt) cc_final: 0.7774 (mmm) REVERT: E 419 ASN cc_start: 0.9008 (m110) cc_final: 0.8644 (m110) REVERT: E 553 ASP cc_start: 0.7982 (m-30) cc_final: 0.7629 (m-30) REVERT: F 551 THR cc_start: 0.8867 (m) cc_final: 0.8640 (t) REVERT: G 455 TYR cc_start: 0.8267 (m-80) cc_final: 0.7456 (m-80) REVERT: G 467 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7597 (mmm-85) REVERT: G 483 ASP cc_start: 0.8769 (m-30) cc_final: 0.8553 (t0) REVERT: G 489 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7403 (ptp) REVERT: G 554 LYS cc_start: 0.7726 (mppt) cc_final: 0.7266 (mtpt) REVERT: H 468 GLU cc_start: 0.8227 (tt0) cc_final: 0.7990 (tp30) REVERT: H 529 ASN cc_start: 0.8345 (m-40) cc_final: 0.7866 (m110) REVERT: K 483 ASP cc_start: 0.7845 (t0) cc_final: 0.7232 (t70) REVERT: L 471 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8236 (m) REVERT: L 487 GLN cc_start: 0.6181 (mt0) cc_final: 0.5775 (mm110) REVERT: L 515 TYR cc_start: 0.7432 (m-80) cc_final: 0.6538 (m-80) REVERT: J 47 GLU cc_start: 0.7860 (mp0) cc_final: 0.7303 (mp0) REVERT: J 117 TYR cc_start: 0.6940 (t80) cc_final: 0.6459 (t80) REVERT: J 125 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7430 (tt0) outliers start: 73 outliers final: 62 residues processed: 335 average time/residue: 0.3597 time to fit residues: 183.5413 Evaluate side-chains 336 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain M residue 409 THR 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 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 522 THR 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 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 554 LYS Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain 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 471 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL 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 114 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 159 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 216 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 345 GLN A 400 HIS B 463 GLN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.192294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133210 restraints weight = 31588.222| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.18 r_work: 0.3556 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21330 Z= 0.124 Angle : 0.601 12.231 29179 Z= 0.304 Chirality : 0.045 0.421 3415 Planarity : 0.005 0.089 3712 Dihedral : 6.074 99.322 3075 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.92 % Allowed : 19.71 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2592 helix: 0.36 (0.23), residues: 490 sheet: -0.42 (0.18), residues: 741 loop : -0.53 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 382 HIS 0.006 0.001 HIS L 518 PHE 0.032 0.002 PHE F 405 TYR 0.035 0.001 TYR L 455 ARG 0.010 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 11) link_NAG-ASN : angle 3.44712 ( 33) link_BETA1-4 : bond 0.01095 ( 1) link_BETA1-4 : angle 2.59563 ( 3) hydrogen bonds : bond 0.03134 ( 598) hydrogen bonds : angle 5.07969 ( 1842) SS BOND : bond 0.00234 ( 27) SS BOND : angle 0.49261 ( 54) covalent geometry : bond 0.00285 (21291) covalent geometry : angle 0.58995 (29089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12126.28 seconds wall clock time: 207 minutes 57.09 seconds (12477.09 seconds total)