Starting phenix.real_space_refine on Thu May 22 09:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yg2_33805/05_2025/7yg2_33805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yg2_33805/05_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_33805/05_2025/7yg2_33805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yg2_33805/05_2025/7yg2_33805.map" model { file = "/net/cci-nas-00/data/ceres_data/7yg2_33805/05_2025/7yg2_33805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yg2_33805/05_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-5687/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: 13.08, per 1000 atoms: 0.63 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: 4.54 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: 2.92 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: 6.54 Time building geometry restraints manager: 5.39 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 45.450 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.370 ------------------------------------------------------------------------------- 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 : 2.393 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: 0.3584 time to fit residues: 212.6459 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 : 2.463 ------------------------------------------------------------------------------- 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 = 0.137445 restraints weight = 31917.919| |-----------------------------------------------------------------------------| 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 3.09782 ( 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 : 2.452 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: 0.7969 (m-80) cc_final: 0.7742 (m-80) REVERT: M 337 TYR cc_start: 0.7008 (p90) cc_final: 0.6789 (p90) REVERT: M 418 TYR cc_start: 0.7729 (t80) cc_final: 0.7522 (t80) REVERT: A 570 ASP cc_start: 0.8001 (t70) cc_final: 0.7732 (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: 0.8395 (mt) REVERT: C 506 MET cc_start: 0.8684 (mtm) cc_final: 0.8252 (mtp) REVERT: D 506 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8336 (mtm) REVERT: E 419 ASN cc_start: 0.8968 (m110) cc_final: 0.8640 (m110) REVERT: F 529 ASN cc_start: 0.7642 (m110) cc_final: 0.6958 (m-40) REVERT: G 455 TYR cc_start: 0.8353 (m-80) cc_final: 0.7706 (m-80) REVERT: G 467 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7398 (mmm-85) REVERT: G 506 MET cc_start: 0.8317 (pmm) cc_final: 0.8022 (pmm) REVERT: G 554 LYS cc_start: 0.7514 (mppt) cc_final: 0.6927 (mttt) REVERT: H 375 TYR cc_start: 0.4195 (t80) cc_final: 0.3931 (t80) REVERT: H 468 GLU cc_start: 0.8109 (tt0) cc_final: 0.7820 (tm-30) REVERT: H 529 ASN cc_start: 0.7917 (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: 0.8462 (m-40) cc_final: 0.8179 (m110) REVERT: K 553 ASP cc_start: 0.7813 (t0) cc_final: 0.7436 (t70) REVERT: L 461 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7476 (mmm-85) REVERT: L 515 TYR cc_start: 0.7793 (m-80) cc_final: 0.7123 (m-80) REVERT: J 51 ASP cc_start: 0.7260 (t70) cc_final: 0.6950 (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: 0.3670 time to fit residues: 190.3023 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 : 2.291 ------------------------------------------------------------------------------- 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: 3.9990 chunk 256 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS 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** ** 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 = 0.4468 r_free = 0.4468 target = 0.195707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141520 restraints weight = 31800.651| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.87 r_work: 0.3558 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21330 Z= 0.166 Angle : 0.587 12.500 29179 Z= 0.300 Chirality : 0.046 0.463 3415 Planarity : 0.004 0.073 3712 Dihedral : 7.780 105.045 3075 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.20 % Allowed : 13.37 % Favored : 84.43 % 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: -0.51 (0.16), residues: 2592 helix: 0.16 (0.23), residues: 486 sheet: -0.19 (0.19), residues: 725 loop : -0.51 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 382 HIS 0.009 0.001 HIS K 430 PHE 0.022 0.002 PHE E 354 TYR 0.030 0.001 TYR L 455 ARG 0.009 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.01061 ( 11) link_NAG-ASN : angle 3.56528 ( 33) link_BETA1-4 : bond 0.00770 ( 1) link_BETA1-4 : angle 2.72380 ( 3) hydrogen bonds : bond 0.03904 ( 598) hydrogen bonds : angle 5.66398 ( 1842) SS BOND : bond 0.00274 ( 27) SS BOND : angle 0.68509 ( 54) covalent geometry : bond 0.00378 (21291) covalent geometry : angle 0.57383 (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 338 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 2.376 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: 0.8011 (m-80) cc_final: 0.7760 (m-80) REVERT: A 570 ASP cc_start: 0.7937 (t70) cc_final: 0.7686 (t0) REVERT: D 506 MET cc_start: 0.8647 (mtp) cc_final: 0.8387 (mtm) REVERT: E 419 ASN cc_start: 0.9018 (m110) cc_final: 0.8657 (m110) REVERT: G 455 TYR cc_start: 0.8343 (m-80) cc_final: 0.7637 (m-80) REVERT: G 489 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7535 (ptp) REVERT: G 554 LYS cc_start: 0.7615 (mppt) cc_final: 0.7058 (mttt) REVERT: H 375 TYR cc_start: 0.4451 (t80) cc_final: 0.4190 (t80) REVERT: H 468 GLU cc_start: 0.8170 (tt0) cc_final: 0.7884 (tp30) REVERT: H 529 ASN cc_start: 0.8030 (m-40) cc_final: 0.7467 (m-40) REVERT: K 410 GLU cc_start: 0.5661 (tm-30) cc_final: 0.5384 (tm-30) REVERT: K 414 CYS cc_start: 0.8137 (t) cc_final: 0.7354 (m) REVERT: K 461 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7237 (mtm-85) REVERT: K 491 ARG cc_start: 0.8046 (mpp-170) cc_final: 0.7839 (mpp-170) REVERT: K 529 ASN cc_start: 0.8457 (m-40) cc_final: 0.8181 (m-40) REVERT: K 553 ASP cc_start: 0.7809 (t0) cc_final: 0.7430 (t70) REVERT: L 461 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7414 (mmm-85) REVERT: L 471 THR cc_start: 0.8698 (m) cc_final: 0.8352 (t) REVERT: L 515 TYR cc_start: 0.7734 (m-80) cc_final: 0.7035 (m-80) REVERT: J 51 ASP cc_start: 0.7592 (t70) cc_final: 0.7362 (t0) REVERT: J 117 TYR cc_start: 0.6512 (t80) cc_final: 0.6264 (t80) outliers start: 52 outliers final: 39 residues processed: 325 average time/residue: 0.3460 time to fit residues: 169.0849 Evaluate side-chains 303 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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 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 538 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 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: 1.9990 chunk 233 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 202 optimal weight: 0.3980 chunk 161 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 400 HIS 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 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS F 439 GLN ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN K 400 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.193462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138400 restraints weight = 32121.099| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.94 r_work: 0.3545 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21330 Z= 0.183 Angle : 0.593 12.202 29179 Z= 0.302 Chirality : 0.046 0.463 3415 Planarity : 0.004 0.069 3712 Dihedral : 7.235 99.960 3075 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.21 % Allowed : 15.14 % Favored : 81.64 % 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: -0.48 (0.16), residues: 2592 helix: 0.24 (0.23), residues: 487 sheet: -0.24 (0.19), residues: 740 loop : -0.48 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 382 HIS 0.009 0.001 HIS L 518 PHE 0.027 0.002 PHE B 424 TYR 0.022 0.001 TYR L 455 ARG 0.010 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 11) link_NAG-ASN : angle 3.56355 ( 33) link_BETA1-4 : bond 0.00734 ( 1) link_BETA1-4 : angle 2.36350 ( 3) hydrogen bonds : bond 0.03609 ( 598) hydrogen bonds : angle 5.48571 ( 1842) SS BOND : bond 0.00302 ( 27) SS BOND : angle 0.61100 ( 54) covalent geometry : bond 0.00426 (21291) covalent geometry : angle 0.58075 (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 360 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 284 time to evaluate : 2.378 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: 0.8172 (m-80) cc_final: 0.7829 (m-80) REVERT: A 346 ARG cc_start: 0.5860 (tpm170) cc_final: 0.5402 (ptp-170) REVERT: A 361 LYS cc_start: 0.7306 (mmtt) cc_final: 0.7001 (mttt) REVERT: A 570 ASP cc_start: 0.8045 (t70) cc_final: 0.7793 (t0) REVERT: B 419 ASN cc_start: 0.8624 (m110) cc_final: 0.8300 (p0) REVERT: B 570 ASP cc_start: 0.6330 (m-30) cc_final: 0.5502 (t0) REVERT: D 506 MET cc_start: 0.8619 (mtp) cc_final: 0.8384 (mtm) REVERT: E 419 ASN cc_start: 0.9054 (m110) cc_final: 0.8679 (m110) REVERT: G 455 TYR cc_start: 0.8422 (m-80) cc_final: 0.7753 (m-80) REVERT: G 467 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7522 (mmm-85) REVERT: G 554 LYS cc_start: 0.7782 (mppt) cc_final: 0.7308 (mtpt) REVERT: H 375 TYR cc_start: 0.4567 (t80) cc_final: 0.4263 (t80) REVERT: H 468 GLU cc_start: 0.8231 (tt0) cc_final: 0.7959 (tp30) REVERT: H 491 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8235 (mtt-85) REVERT: H 529 ASN cc_start: 0.8187 (m-40) cc_final: 0.7601 (m110) REVERT: K 461 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7228 (mtm-85) REVERT: K 529 ASN cc_start: 0.8414 (m-40) cc_final: 0.8172 (m-40) REVERT: K 553 ASP cc_start: 0.7973 (t0) cc_final: 0.7766 (t0) REVERT: L 515 TYR cc_start: 0.7689 (m-80) cc_final: 0.6956 (m-80) REVERT: L 519 SER cc_start: 0.8478 (m) cc_final: 0.7679 (t) REVERT: L 520 ILE cc_start: 0.7913 (mt) cc_final: 0.7711 (mt) REVERT: J 51 ASP cc_start: 0.7962 (t70) cc_final: 0.7654 (t0) REVERT: J 117 TYR cc_start: 0.6645 (t80) cc_final: 0.6299 (t80) outliers start: 76 outliers final: 56 residues processed: 342 average time/residue: 0.3638 time to fit residues: 184.3309 Evaluate side-chains 324 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 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 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 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 499 LYS Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain L residue 571 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 49 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 465 ASN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.193542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.139509 restraints weight = 31902.711| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.43 r_work: 0.3575 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21330 Z= 0.144 Angle : 0.569 11.944 29179 Z= 0.288 Chirality : 0.046 0.447 3415 Planarity : 0.004 0.074 3712 Dihedral : 6.915 100.550 3075 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 16.12 % Favored : 80.71 % 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: -0.40 (0.16), residues: 2592 helix: 0.37 (0.24), residues: 485 sheet: -0.23 (0.19), residues: 744 loop : -0.42 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 382 HIS 0.007 0.001 HIS L 518 PHE 0.023 0.002 PHE M 346 TYR 0.020 0.001 TYR M 418 ARG 0.009 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 11) link_NAG-ASN : angle 3.48373 ( 33) link_BETA1-4 : bond 0.01080 ( 1) link_BETA1-4 : angle 2.44494 ( 3) hydrogen bonds : bond 0.03334 ( 598) hydrogen bonds : angle 5.29396 ( 1842) SS BOND : bond 0.00232 ( 27) SS BOND : angle 0.53930 ( 54) covalent geometry : bond 0.00334 (21291) covalent geometry : angle 0.55682 (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 358 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 2.265 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: 0.8157 (m-10) cc_final: 0.7820 (m-80) REVERT: A 361 LYS cc_start: 0.7334 (mmtt) cc_final: 0.6938 (mttt) REVERT: B 554 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8358 (mtpt) REVERT: B 570 ASP cc_start: 0.6362 (m-30) cc_final: 0.5639 (t0) REVERT: C 358 PHE cc_start: 0.8343 (t80) cc_final: 0.7744 (t80) REVERT: C 424 PHE cc_start: 0.6384 (m-10) cc_final: 0.6041 (m-10) REVERT: D 506 MET cc_start: 0.8485 (mtp) cc_final: 0.8235 (mtm) REVERT: E 419 ASN cc_start: 0.9044 (m110) cc_final: 0.8656 (m110) REVERT: E 568 MET cc_start: 0.6240 (tpt) cc_final: 0.5935 (tpp) REVERT: F 551 THR cc_start: 0.8745 (m) cc_final: 0.8505 (t) REVERT: G 455 TYR cc_start: 0.8373 (m-80) cc_final: 0.7675 (m-80) REVERT: G 467 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7680 (mmm-85) REVERT: G 489 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7426 (ptp) REVERT: G 554 LYS cc_start: 0.7759 (mppt) cc_final: 0.7218 (mttt) REVERT: H 370 THR cc_start: -0.0178 (OUTLIER) cc_final: -0.0600 (p) REVERT: H 375 TYR cc_start: 0.4615 (t80) cc_final: 0.4304 (t80) REVERT: H 468 GLU cc_start: 0.8208 (tt0) cc_final: 0.7965 (tp30) REVERT: H 491 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8191 (mtt-85) REVERT: H 529 ASN cc_start: 0.8271 (m-40) cc_final: 0.7689 (m110) REVERT: K 529 ASN cc_start: 0.8395 (m-40) cc_final: 0.8158 (m-40) REVERT: L 487 GLN cc_start: 0.6184 (mt0) cc_final: 0.5828 (mm110) REVERT: L 515 TYR cc_start: 0.7670 (m-80) cc_final: 0.6941 (m-80) REVERT: L 519 SER cc_start: 0.8486 (m) cc_final: 0.7540 (t) REVERT: J 109 TYR cc_start: 0.7608 (m-80) cc_final: 0.7390 (m-80) REVERT: J 117 TYR cc_start: 0.6568 (t80) cc_final: 0.6250 (t80) outliers start: 75 outliers final: 55 residues processed: 341 average time/residue: 0.3472 time to fit residues: 176.0734 Evaluate side-chains 318 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain M residue 397 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 396 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 165 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 186 optimal weight: 0.0670 overall best weight: 2.1524 ------------------------------------------------------------------------------- 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 490 GLN 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 ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN F 487 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 = 0.4385 r_free = 0.4385 target = 0.188056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126525 restraints weight = 31689.541| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.22 r_work: 0.3481 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21330 Z= 0.267 Angle : 0.672 12.226 29179 Z= 0.345 Chirality : 0.049 0.479 3415 Planarity : 0.005 0.076 3712 Dihedral : 7.186 101.487 3075 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.06 % Allowed : 16.75 % Favored : 79.19 % 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: -0.74 (0.16), residues: 2592 helix: 0.15 (0.23), residues: 485 sheet: -0.53 (0.18), residues: 740 loop : -0.61 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 382 HIS 0.015 0.001 HIS D 400 PHE 0.024 0.002 PHE A 479 TYR 0.024 0.002 TYR L 455 ARG 0.011 0.001 ARG M 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 11) link_NAG-ASN : angle 3.66388 ( 33) link_BETA1-4 : bond 0.00886 ( 1) link_BETA1-4 : angle 2.33438 ( 3) hydrogen bonds : bond 0.04015 ( 598) hydrogen bonds : angle 5.68022 ( 1842) SS BOND : bond 0.00482 ( 27) SS BOND : angle 0.79147 ( 54) covalent geometry : bond 0.00631 (21291) covalent geometry : angle 0.66042 (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 389 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 293 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 235 TYR cc_start: 0.8254 (m-10) cc_final: 0.7949 (m-80) REVERT: A 361 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7182 (mttt) REVERT: A 570 ASP cc_start: 0.8353 (t0) cc_final: 0.8094 (t0) REVERT: B 419 ASN cc_start: 0.8675 (m110) cc_final: 0.8342 (p0) REVERT: B 570 ASP cc_start: 0.6629 (m-30) cc_final: 0.6036 (t0) REVERT: E 419 ASN cc_start: 0.9052 (m110) cc_final: 0.8659 (m110) REVERT: F 414 CYS cc_start: 0.6801 (t) cc_final: 0.6596 (t) REVERT: G 489 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7502 (ptp) REVERT: G 493 GLN cc_start: 0.8073 (mm110) cc_final: 0.7254 (pp30) REVERT: G 554 LYS cc_start: 0.8014 (mppt) cc_final: 0.7629 (mtpt) REVERT: H 370 THR cc_start: -0.0156 (OUTLIER) cc_final: -0.0620 (p) REVERT: H 468 GLU cc_start: 0.8203 (tt0) cc_final: 0.7972 (tp30) REVERT: H 529 ASN cc_start: 0.8212 (m-40) cc_final: 0.7719 (m110) REVERT: K 518 HIS cc_start: 0.7798 (m-70) cc_final: 0.7420 (m-70) REVERT: K 529 ASN cc_start: 0.8373 (m-40) cc_final: 0.8155 (m-40) REVERT: L 515 TYR cc_start: 0.7633 (m-80) cc_final: 0.6791 (m-80) REVERT: L 519 SER cc_start: 0.8578 (m) cc_final: 0.7768 (t) REVERT: L 553 ASP cc_start: 0.7100 (m-30) cc_final: 0.6823 (m-30) REVERT: J 41 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8920 (m) REVERT: J 117 TYR cc_start: 0.7130 (t80) cc_final: 0.6793 (t80) outliers start: 96 outliers final: 70 residues processed: 368 average time/residue: 0.3523 time to fit residues: 190.8466 Evaluate side-chains 339 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 266 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 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 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 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 551 THR Chi-restraints excluded: chain E residue 553 ASP 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 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 456 LEU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 41 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 204 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 203 optimal weight: 0.4980 chunk 208 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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 545 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS C 465 ASN ** E 518 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.126345 restraints weight = 31427.161| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.17 r_work: 0.3459 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4930 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= 0.291 Angle : 0.680 12.904 29179 Z= 0.349 Chirality : 0.049 0.477 3415 Planarity : 0.005 0.090 3712 Dihedral : 7.160 101.779 3075 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.31 % Allowed : 17.09 % Favored : 78.60 % 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: -0.88 (0.16), residues: 2592 helix: 0.07 (0.23), residues: 485 sheet: -0.68 (0.18), residues: 753 loop : -0.67 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 382 HIS 0.007 0.001 HIS D 400 PHE 0.024 0.002 PHE K 479 TYR 0.041 0.002 TYR L 455 ARG 0.011 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 11) link_NAG-ASN : angle 3.76540 ( 33) link_BETA1-4 : bond 0.00126 ( 1) link_BETA1-4 : angle 2.25870 ( 3) hydrogen bonds : bond 0.03994 ( 598) hydrogen bonds : angle 5.77965 ( 1842) SS BOND : bond 0.00482 ( 27) SS BOND : angle 0.87562 ( 54) covalent geometry : bond 0.00692 (21291) covalent geometry : angle 0.66812 (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 376 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 274 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8300 (m-10) cc_final: 0.8019 (m-80) REVERT: M 300 ASN cc_start: 0.8445 (t0) cc_final: 0.8103 (t0) REVERT: A 361 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7184 (mttt) REVERT: A 570 ASP cc_start: 0.8410 (t0) cc_final: 0.8054 (t0) REVERT: B 570 ASP cc_start: 0.6692 (m-30) cc_final: 0.6215 (t0) REVERT: C 376 ASP cc_start: 0.5115 (m-30) cc_final: 0.4865 (m-30) REVERT: C 467 ARG cc_start: 0.7712 (mmt180) cc_final: 0.7461 (mmt180) REVERT: E 419 ASN cc_start: 0.8972 (m110) cc_final: 0.8586 (m110) REVERT: E 553 ASP cc_start: 0.7934 (m-30) cc_final: 0.7497 (m-30) REVERT: G 489 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7448 (ptp) REVERT: G 526 GLU cc_start: 0.7661 (mp0) cc_final: 0.7322 (mp0) REVERT: G 554 LYS cc_start: 0.7915 (mppt) cc_final: 0.7448 (mtpt) REVERT: H 370 THR cc_start: -0.0402 (OUTLIER) cc_final: -0.0755 (p) REVERT: H 375 TYR cc_start: 0.4270 (t80) cc_final: 0.4062 (t80) REVERT: H 468 GLU cc_start: 0.8204 (tt0) cc_final: 0.7999 (tp30) REVERT: H 529 ASN cc_start: 0.8239 (m-40) cc_final: 0.7718 (m110) REVERT: K 529 ASN cc_start: 0.8355 (m-40) cc_final: 0.8133 (m-40) REVERT: L 487 GLN cc_start: 0.6172 (mt0) cc_final: 0.5929 (mm110) REVERT: L 515 TYR cc_start: 0.7510 (m-80) cc_final: 0.6544 (m-80) REVERT: L 519 SER cc_start: 0.8551 (m) cc_final: 0.7693 (t) REVERT: L 520 ILE cc_start: 0.8338 (mt) cc_final: 0.8112 (mt) REVERT: J 117 TYR cc_start: 0.7273 (t80) cc_final: 0.6857 (t80) REVERT: J 125 GLU cc_start: 0.7819 (tt0) cc_final: 0.7591 (tt0) outliers start: 102 outliers final: 77 residues processed: 355 average time/residue: 0.3507 time to fit residues: 186.3563 Evaluate side-chains 346 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 267 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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 503 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 361 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 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 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 547 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 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 484 VAL 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 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 564 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 524 SER Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain 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: 0.9990 chunk 180 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 326 GLN A 400 HIS A 545 ASN 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.190495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130729 restraints weight = 31707.458| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.20 r_work: 0.3522 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21330 Z= 0.147 Angle : 0.609 11.515 29179 Z= 0.312 Chirality : 0.046 0.419 3415 Planarity : 0.005 0.087 3712 Dihedral : 6.734 101.005 3075 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.64 % Allowed : 18.23 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.16), residues: 2592 helix: 0.25 (0.23), residues: 483 sheet: -0.57 (0.18), residues: 758 loop : -0.62 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 382 HIS 0.006 0.001 HIS D 400 PHE 0.042 0.002 PHE F 405 TYR 0.034 0.001 TYR L 455 ARG 0.012 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 11) link_NAG-ASN : angle 3.63802 ( 33) link_BETA1-4 : bond 0.00673 ( 1) link_BETA1-4 : angle 2.07365 ( 3) hydrogen bonds : bond 0.03399 ( 598) hydrogen bonds : angle 5.43780 ( 1842) SS BOND : bond 0.00266 ( 27) SS BOND : angle 0.67080 ( 54) covalent geometry : bond 0.00342 (21291) covalent geometry : angle 0.59662 (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 364 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 278 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 235 TYR cc_start: 0.8239 (m-10) cc_final: 0.8036 (m-80) REVERT: M 300 ASN cc_start: 0.8430 (t0) cc_final: 0.8072 (t0) REVERT: A 361 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7143 (mttt) REVERT: A 499 LYS cc_start: 0.9221 (tttm) cc_final: 0.8977 (ttmt) REVERT: A 570 ASP cc_start: 0.8416 (t0) cc_final: 0.8019 (t0) REVERT: B 419 ASN cc_start: 0.8594 (m110) cc_final: 0.8231 (p0) REVERT: B 443 ARG cc_start: 0.7539 (ttm110) cc_final: 0.7249 (ttm110) REVERT: B 451 ARG cc_start: 0.8733 (ptm-80) cc_final: 0.8338 (ptp90) REVERT: C 376 ASP cc_start: 0.5090 (m-30) cc_final: 0.4842 (m-30) REVERT: E 419 ASN cc_start: 0.9004 (m110) cc_final: 0.8641 (m110) REVERT: E 553 ASP cc_start: 0.7844 (m-30) cc_final: 0.7503 (m-30) REVERT: G 455 TYR cc_start: 0.8307 (m-80) cc_final: 0.7502 (m-80) REVERT: G 489 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7424 (ptp) REVERT: G 526 GLU cc_start: 0.7493 (mp0) cc_final: 0.7136 (mp0) REVERT: G 554 LYS cc_start: 0.7873 (mppt) cc_final: 0.7389 (mtpt) REVERT: H 370 THR cc_start: -0.0161 (OUTLIER) cc_final: -0.0483 (p) REVERT: H 529 ASN cc_start: 0.8270 (m-40) cc_final: 0.7801 (m110) REVERT: K 479 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: K 490 GLN cc_start: 0.7268 (mm110) cc_final: 0.7059 (mm110) REVERT: K 498 GLU cc_start: 0.8056 (mp0) cc_final: 0.7747 (mp0) REVERT: L 487 GLN cc_start: 0.6034 (mt0) cc_final: 0.5732 (mm110) REVERT: L 515 TYR cc_start: 0.7475 (m-80) cc_final: 0.6553 (m-80) REVERT: J 117 TYR cc_start: 0.7001 (t80) cc_final: 0.6592 (t80) outliers start: 86 outliers final: 70 residues processed: 345 average time/residue: 0.3471 time to fit residues: 180.2011 Evaluate side-chains 340 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 361 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 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 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 547 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 566 LEU Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 483 ASP Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS 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 524 SER Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 226 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 257 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 A 545 ASN B 393 HIS B 463 GLN B 529 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.188760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134147 restraints weight = 30949.075| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.62 r_work: 0.3502 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21330 Z= 0.166 Angle : 0.615 13.494 29179 Z= 0.312 Chirality : 0.046 0.435 3415 Planarity : 0.005 0.091 3712 Dihedral : 6.546 100.577 3075 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.51 % Allowed : 18.53 % Favored : 77.96 % 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: 0.24 (0.23), residues: 484 sheet: -0.57 (0.18), residues: 761 loop : -0.60 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 382 HIS 0.012 0.001 HIS B 393 PHE 0.035 0.002 PHE F 405 TYR 0.051 0.002 TYR L 455 ARG 0.011 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 11) link_NAG-ASN : angle 3.61581 ( 33) link_BETA1-4 : bond 0.00827 ( 1) link_BETA1-4 : angle 2.38517 ( 3) hydrogen bonds : bond 0.03414 ( 598) hydrogen bonds : angle 5.40530 ( 1842) SS BOND : bond 0.00305 ( 27) SS BOND : angle 0.60136 ( 54) covalent geometry : bond 0.00393 (21291) covalent geometry : angle 0.60323 (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 363 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: M 235 TYR cc_start: 0.8266 (m-10) cc_final: 0.8061 (m-80) REVERT: M 300 ASN cc_start: 0.8452 (t0) cc_final: 0.8103 (t0) REVERT: A 361 LYS cc_start: 0.7515 (mmtt) cc_final: 0.7139 (mttt) REVERT: A 499 LYS cc_start: 0.9219 (tttm) cc_final: 0.8945 (tttm) REVERT: A 570 ASP cc_start: 0.8420 (t0) cc_final: 0.8202 (t0) REVERT: B 419 ASN cc_start: 0.8555 (m110) cc_final: 0.8185 (p0) REVERT: B 443 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7277 (ttm110) REVERT: B 451 ARG cc_start: 0.8725 (ptm-80) cc_final: 0.8292 (ptp90) REVERT: C 376 ASP cc_start: 0.5095 (m-30) cc_final: 0.4849 (m-30) REVERT: E 419 ASN cc_start: 0.9008 (m110) cc_final: 0.8642 (m110) REVERT: E 553 ASP cc_start: 0.7932 (m-30) cc_final: 0.7574 (m-30) REVERT: G 455 TYR cc_start: 0.8337 (m-80) cc_final: 0.7536 (m-80) REVERT: G 467 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7601 (mmm-85) REVERT: G 489 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7479 (ptp) REVERT: G 526 GLU cc_start: 0.7493 (mp0) cc_final: 0.7122 (mp0) REVERT: G 554 LYS cc_start: 0.7851 (mppt) cc_final: 0.7370 (mtpt) REVERT: H 370 THR cc_start: -0.0197 (OUTLIER) cc_final: -0.0549 (p) REVERT: H 529 ASN cc_start: 0.8314 (m-40) cc_final: 0.7851 (m110) REVERT: K 479 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: K 490 GLN cc_start: 0.7363 (mm110) cc_final: 0.7153 (mm110) REVERT: K 498 GLU cc_start: 0.8027 (mp0) cc_final: 0.7764 (mp0) REVERT: L 471 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8458 (m) REVERT: L 487 GLN cc_start: 0.6073 (mt0) cc_final: 0.5736 (mm110) REVERT: L 515 TYR cc_start: 0.7499 (m-80) cc_final: 0.6578 (m-80) REVERT: J 47 GLU cc_start: 0.8143 (mp0) cc_final: 0.7350 (mp0) REVERT: J 117 TYR cc_start: 0.7018 (t80) cc_final: 0.6582 (t80) REVERT: J 125 GLU cc_start: 0.7979 (tt0) cc_final: 0.7774 (tt0) outliers start: 83 outliers final: 72 residues processed: 345 average time/residue: 0.3603 time to fit residues: 188.0061 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 : 2.765 ------------------------------------------------------------------------------- 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 518 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 361 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 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 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 566 LEU 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 522 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 561 LEU Chi-restraints excluded: chain K residue 393 HIS Chi-restraints excluded: chain K residue 473 THR 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 471 THR Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 564 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 37 optimal weight: 0.0170 chunk 70 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 248 optimal weight: 0.6980 chunk 42 optimal weight: 0.0040 chunk 255 optimal weight: 0.0570 chunk 136 optimal weight: 0.7980 overall best weight: 0.2348 ------------------------------------------------------------------------------- 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 A 545 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 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 = 0.4422 r_free = 0.4422 target = 0.191476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137035 restraints weight = 30825.235| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.37 r_work: 0.3554 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21330 Z= 0.112 Angle : 0.593 12.505 29179 Z= 0.301 Chirality : 0.045 0.403 3415 Planarity : 0.005 0.086 3712 Dihedral : 6.114 99.870 3075 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.66 % Allowed : 19.42 % Favored : 77.92 % 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: -0.56 (0.16), residues: 2592 helix: 0.34 (0.23), residues: 489 sheet: -0.37 (0.19), residues: 724 loop : -0.54 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 382 HIS 0.005 0.001 HIS E 540 PHE 0.035 0.001 PHE F 405 TYR 0.039 0.001 TYR L 455 ARG 0.011 0.001 ARG B 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 11) link_NAG-ASN : angle 3.49560 ( 33) link_BETA1-4 : bond 0.01256 ( 1) link_BETA1-4 : angle 2.81576 ( 3) hydrogen bonds : bond 0.03120 ( 598) hydrogen bonds : angle 5.12783 ( 1842) SS BOND : bond 0.00227 ( 27) SS BOND : angle 0.52865 ( 54) covalent geometry : bond 0.00249 (21291) covalent geometry : angle 0.58055 (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 348 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: M 300 ASN cc_start: 0.8431 (t0) cc_final: 0.8178 (t0) REVERT: M 321 MET cc_start: 0.7839 (ttt) cc_final: 0.7560 (ptm) REVERT: A 361 LYS cc_start: 0.7439 (mmtt) cc_final: 0.6995 (mttt) REVERT: A 499 LYS cc_start: 0.9210 (tttm) cc_final: 0.8941 (tttm) REVERT: B 419 ASN cc_start: 0.8586 (m110) cc_final: 0.8206 (p0) REVERT: B 443 ARG cc_start: 0.7525 (ttm110) cc_final: 0.7256 (ttm110) REVERT: B 451 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8322 (ptp90) REVERT: C 376 ASP cc_start: 0.5078 (m-30) cc_final: 0.4864 (m-30) REVERT: D 506 MET cc_start: 0.8410 (mtm) cc_final: 0.8113 (mtp) REVERT: E 419 ASN cc_start: 0.8992 (m110) cc_final: 0.8628 (m110) REVERT: E 553 ASP cc_start: 0.7888 (m-30) cc_final: 0.7501 (m-30) REVERT: E 562 TYR cc_start: 0.8159 (p90) cc_final: 0.7893 (p90) REVERT: F 551 THR cc_start: 0.8757 (m) cc_final: 0.8535 (t) REVERT: G 455 TYR cc_start: 0.8165 (m-80) cc_final: 0.7348 (m-80) REVERT: G 483 ASP cc_start: 0.8817 (m-30) cc_final: 0.8566 (t0) REVERT: G 489 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7403 (ptp) REVERT: G 526 GLU cc_start: 0.7408 (mp0) cc_final: 0.7081 (mp0) REVERT: G 554 LYS cc_start: 0.7629 (mppt) cc_final: 0.7164 (mtpt) REVERT: H 370 THR cc_start: 0.0017 (OUTLIER) cc_final: -0.0286 (p) REVERT: H 529 ASN cc_start: 0.8280 (m-40) cc_final: 0.7800 (m110) REVERT: K 483 ASP cc_start: 0.7837 (t0) cc_final: 0.7219 (t70) REVERT: K 498 GLU cc_start: 0.7962 (mp0) cc_final: 0.7717 (mp0) REVERT: L 487 GLN cc_start: 0.6100 (mt0) cc_final: 0.5763 (mm110) REVERT: L 515 TYR cc_start: 0.7459 (m-80) cc_final: 0.6630 (m-80) REVERT: J 47 GLU cc_start: 0.7717 (mp0) cc_final: 0.7158 (mp0) REVERT: J 117 TYR cc_start: 0.6856 (t80) cc_final: 0.6447 (t80) outliers start: 63 outliers final: 51 residues processed: 330 average time/residue: 0.3418 time to fit residues: 169.9380 Evaluate side-chains 322 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 237 TYR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 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 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain D residue 393 HIS Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain H residue 367 CYS Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 483 ASP 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 L residue 347 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 524 SER Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 114 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 216 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.192627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136671 restraints weight = 31598.991| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.49 r_work: 0.3536 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21330 Z= 0.132 Angle : 0.596 12.401 29179 Z= 0.302 Chirality : 0.045 0.410 3415 Planarity : 0.005 0.088 3712 Dihedral : 6.022 99.238 3075 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.62 % Allowed : 19.63 % Favored : 77.75 % 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: -0.51 (0.16), residues: 2592 helix: 0.38 (0.23), residues: 489 sheet: -0.36 (0.19), residues: 730 loop : -0.49 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 382 HIS 0.005 0.001 HIS L 518 PHE 0.033 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 0.00554 ( 11) link_NAG-ASN : angle 3.40417 ( 33) link_BETA1-4 : bond 0.01158 ( 1) link_BETA1-4 : angle 2.66796 ( 3) hydrogen bonds : bond 0.03171 ( 598) hydrogen bonds : angle 5.09870 ( 1842) SS BOND : bond 0.00266 ( 27) SS BOND : angle 0.48459 ( 54) covalent geometry : bond 0.00308 (21291) covalent geometry : angle 0.58485 (29089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11858.22 seconds wall clock time: 205 minutes 43.70 seconds (12343.70 seconds total)