Starting phenix.real_space_refine on Sat Jul 4 12:59:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y09_33538/07_2026/7y09_33538.map" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 13105 2.51 5 N 3538 2.21 5 O 4070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20817 Number of models: 1 Model: "" Number of chains: 23 Chain: "R" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2291 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 1 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: {'PCIS': 1, 'PTRANS': 17, '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: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.84, per 1000 atoms: 0.23 Number of scatterers: 20817 At special positions: 0 Unit cell: (91.8, 174.96, 195.48, 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 104 16.00 O 4070 8.00 N 3538 7.00 C 13105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 164 " 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=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 831.1 milliseconds 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5060 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 57 sheets defined 19.3% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'R' and resid 157 through 162 Processing helix chain 'R' and resid 165 through 171 removed outlier: 4.048A pdb=" N VAL R 171 " --> pdb=" O ASN R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 204 Processing helix chain 'R' and resid 207 through 224 Processing helix chain 'R' and resid 230 through 245 Processing helix chain 'R' and resid 248 through 280 removed outlier: 5.509A pdb=" N SER R 265 " --> pdb=" O GLU R 261 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE R 267 " --> pdb=" O ASN R 263 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 323 Processing helix chain 'R' and resid 341 through 372 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 373 through 376 removed outlier: 4.433A pdb=" N TYR R 376 " --> pdb=" O LYS R 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 373 through 376' Processing helix chain 'R' and resid 377 through 381 removed outlier: 4.342A pdb=" N SER R 381 " --> pdb=" O ASP R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 392 removed outlier: 3.802A pdb=" N ILE R 391 " --> pdb=" O TYR R 387 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.591A pdb=" N TRP A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.742A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.666A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.604A pdb=" N LEU B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.944A pdb=" N LEU C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 530 removed outlier: 3.686A pdb=" N ASN C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 525 through 530' Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.667A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 460 through 467 removed outlier: 3.566A pdb=" N LEU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 removed outlier: 3.613A pdb=" N TRP D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.583A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.760A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.793A 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 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 420 removed outlier: 3.575A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 361 removed outlier: 3.649A pdb=" N THR G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.574A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 removed outlier: 3.588A pdb=" N THR G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 558 removed outlier: 3.525A pdb=" N GLY G 557 " --> pdb=" O ASP G 553 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 558 " --> pdb=" O LYS G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 558' Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 removed outlier: 4.069A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 removed outlier: 3.731A pdb=" N LEU H 466 " --> pdb=" O GLU H 462 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG H 467 " --> pdb=" O GLN H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 531 removed outlier: 3.532A pdb=" N TRP H 528 " --> pdb=" O SER H 524 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 529 " --> pdb=" O GLU H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 557 removed outlier: 3.576A pdb=" N THR H 556 " --> pdb=" O ASP H 553 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 553 through 557' Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.997A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 420 Processing helix chain 'K' and resid 460 through 467 removed outlier: 3.594A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG K 467 " --> pdb=" O GLN K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 530 Processing helix chain 'L' and resid 355 through 360 Processing helix chain 'L' and resid 414 through 420 removed outlier: 4.275A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 467 removed outlier: 3.693A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 530 removed outlier: 3.683A pdb=" N THR L 530 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.590A pdb=" N CYS J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 64 through 69' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 4.156A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 383 removed outlier: 3.667A pdb=" N TRP A 382 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS A 391 " --> pdb=" O TRP A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 424 through 427 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.628A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.628A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.934A 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: 3.575A pdb=" N VAL A 538 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 548 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 561 through 562 removed outlier: 3.574A pdb=" N TYR B 562 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER B 565 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 564 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL B 567 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 566 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER B 569 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A 568 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE J 60 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER A 565 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR J 62 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.567A pdb=" N ILE B 350 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 379 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 455 through 457 removed outlier: 3.809A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 455 through 457 removed outlier: 3.809A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.537A pdb=" N PHE B 485 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 487 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.528A pdb=" N ILE C 350 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 369 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.528A pdb=" N ILE C 350 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 363 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 413 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 365 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 411 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.858A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 429 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 441 " --> pdb=" O PHE C 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.821A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.821A pdb=" N THR C 477 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.515A pdb=" N PHE C 485 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 565 through 566 removed outlier: 3.857A pdb=" N VAL D 567 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 567 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.626A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 365 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 411 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS D 367 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY D 409 " --> pdb=" O CYS D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 378 through 383 Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.619A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.619A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.919A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE E 405 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 424 through 428 removed outlier: 3.636A pdb=" N ILE E 441 " --> pdb=" O PHE E 424 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY E 478 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.631A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY E 478 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 493 through 494 removed outlier: 3.549A pdb=" N PHE E 485 " --> pdb=" O ALA E 539 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 487 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 537 " --> pdb=" O GLN E 487 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET E 489 " --> pdb=" O THR E 535 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR E 535 " --> pdb=" O MET E 489 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 363 through 365 removed outlier: 3.562A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 379 through 384 removed outlier: 3.609A pdb=" N THR F 379 " --> pdb=" O THR F 429 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.613A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 501 " --> pdb=" O ILE F 520 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.613A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.597A pdb=" N PHE F 485 " --> pdb=" O ALA F 539 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 539 " --> pdb=" O PHE F 485 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.078A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER H 565 " --> pdb=" O LEU K 566 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER L 565 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.749A pdb=" N ILE G 350 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 424 through 428 Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.616A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE G 520 " --> pdb=" O VAL G 501 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 501 " --> pdb=" O ILE G 520 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.187A pdb=" N THR G 477 " --> pdb=" O ALA G 517 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA G 517 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE G 479 " --> pdb=" O TYR G 515 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE5, first strand: chain 'H' and resid 346 through 350 removed outlier: 3.757A pdb=" N LEU H 368 " --> pdb=" O PHE H 348 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE H 350 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.656A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H 441 " --> pdb=" O PHE H 424 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.727A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.731A pdb=" N VAL H 538 " --> pdb=" O THR H 548 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR H 548 " --> pdb=" O VAL H 538 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA K 407 " --> pdb=" O VAL K 369 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.535A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS K 426 " --> pdb=" O GLN K 439 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.541A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.541A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AF6, first strand: chain 'K' and resid 561 through 562 removed outlier: 7.408A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG J 35 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER J 19 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 369 through 372 removed outlier: 5.275A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 379 through 384 removed outlier: 4.330A pdb=" N THR L 379 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR L 429 " --> pdb=" O THR L 379 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 453 through 456 removed outlier: 4.094A pdb=" N SER L 519 " --> pdb=" O CYS L 474 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL L 501 " --> pdb=" O ILE L 520 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 453 through 456 removed outlier: 5.794A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 493 through 494 removed outlier: 3.550A pdb=" N GLN L 490 " --> pdb=" O GLN L 493 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR L 548 " --> pdb=" O VAL L 538 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 110 through 116 removed outlier: 3.836A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2013 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: 4.22 Time building geometry restraints manager: 2.28 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: 6753 1.34 - 1.46: 4786 1.46 - 1.58: 9648 1.58 - 1.70: 0 1.70 - 1.82: 139 Bond restraints: 21326 Sorted by residual: bond pdb=" C1 NAG H 601 " pdb=" O5 NAG H 601 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C SER K 480 " pdb=" N PRO K 481 " ideal model delta sigma weight residual 1.336 1.365 -0.030 1.08e-02 8.57e+03 7.50e+00 bond pdb=" C1 NAG L 601 " pdb=" O5 NAG L 601 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C1 NAG F 601 " pdb=" O5 NAG F 601 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.54e+00 ... (remaining 21321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 28528 2.15 - 4.31: 544 4.31 - 6.46: 46 6.46 - 8.61: 9 8.61 - 10.77: 2 Bond angle restraints: 29129 Sorted by residual: angle pdb=" N CYS J 14 " pdb=" CA CYS J 14 " pdb=" C CYS J 14 " ideal model delta sigma weight residual 112.86 108.11 4.75 1.22e+00 6.72e-01 1.52e+01 angle pdb=" CB MET L 568 " pdb=" CG MET L 568 " pdb=" SD MET L 568 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CG MET R 272 " pdb=" SD MET R 272 " pdb=" CE MET R 272 " ideal model delta sigma weight residual 100.90 93.18 7.72 2.20e+00 2.07e-01 1.23e+01 angle pdb=" CA ASN K 563 " pdb=" CB ASN K 563 " pdb=" CG ASN K 563 " ideal model delta sigma weight residual 112.60 115.99 -3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" CA ASN L 563 " pdb=" CB ASN L 563 " pdb=" CG ASN L 563 " ideal model delta sigma weight residual 112.60 115.90 -3.30 1.00e+00 1.00e+00 1.09e+01 ... (remaining 29124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 11644 17.41 - 34.82: 979 34.82 - 52.23: 183 52.23 - 69.64: 40 69.64 - 87.05: 29 Dihedral angle restraints: 12875 sinusoidal: 5120 harmonic: 7755 Sorted by residual: dihedral pdb=" CB CYS J 108 " pdb=" SG CYS J 108 " pdb=" SG CYS J 133 " pdb=" CB CYS J 133 " ideal model delta sinusoidal sigma weight residual -86.00 -153.22 67.22 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS L 474 " pdb=" SG CYS L 474 " pdb=" SG CYS L 536 " pdb=" CB CYS L 536 " ideal model delta sinusoidal sigma weight residual 93.00 156.32 -63.32 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS G 367 " pdb=" SG CYS G 367 " pdb=" SG CYS G 426 " pdb=" CB CYS G 426 " ideal model delta sinusoidal sigma weight residual 93.00 145.22 -52.22 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 12872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3398 0.142 - 0.285: 14 0.285 - 0.427: 1 0.427 - 0.569: 0 0.569 - 0.711: 2 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 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 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 -1.78 -0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN J 48 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 3412 not shown) Planarity restraints: 3727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.030 2.00e-02 2.50e+03 2.83e-02 9.99e+00 pdb=" CG ASN K 563 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 400 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO C 401 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 401 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 401 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 563 " 0.026 2.00e-02 2.50e+03 2.39e-02 7.12e+00 pdb=" CG ASN G 563 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN G 563 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN G 563 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG G 601 " 0.028 2.00e-02 2.50e+03 ... (remaining 3724 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1887 2.75 - 3.29: 20435 3.29 - 3.83: 33943 3.83 - 4.36: 38711 4.36 - 4.90: 66634 Nonbonded interactions: 161610 Sorted by model distance: nonbonded pdb=" OG1 THR F 383 " pdb=" OG1 THR F 425 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR C 363 " pdb=" O ILE C 413 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR F 363 " pdb=" O ILE F 413 " model vdw 2.260 3.040 nonbonded pdb=" O SER A 356 " pdb=" OG1 THR A 360 " model vdw 2.260 3.040 nonbonded pdb=" O ALA H 448 " pdb=" OG SER H 480 " model vdw 2.264 3.040 ... (remaining 161605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.250 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.065 21361 Z= 0.153 Angle : 0.697 12.439 29211 Z= 0.363 Chirality : 0.050 0.711 3415 Planarity : 0.006 0.077 3716 Dihedral : 13.891 87.046 7746 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.13 % Allowed : 0.25 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2600 helix: -0.50 (0.23), residues: 438 sheet: 0.46 (0.18), residues: 799 loop : -0.56 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 491 TYR 0.033 0.002 TYR R 376 PHE 0.025 0.002 PHE C 405 TRP 0.031 0.002 TRP R 362 HIS 0.013 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (21326) covalent geometry : angle 0.67226 / 0.36 (29129) SS BOND : bond 0.00164 / 0.10 ( 23) SS BOND : angle 1.29201 / 0.91 ( 46) hydrogen bonds : bond 0.25599 / 16.72 ( 666) hydrogen bonds : angle 9.86242 / 7.08 ( 2013) link_BETA1-4 : bond 0.00961 / 0.64 ( 1) link_BETA1-4 : angle 1.25793 / 0.96 ( 3) link_NAG-ASN : bond 0.01214 / 0.79 ( 11) link_NAG-ASN : angle 5.34192 / 3.29 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 436 time to evaluate : 0.760 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: R 260 TRP cc_start: 0.8255 (t60) cc_final: 0.7636 (t60) REVERT: R 268 TRP cc_start: 0.8068 (t-100) cc_final: 0.7659 (t-100) REVERT: R 278 HIS cc_start: 0.8567 (t-90) cc_final: 0.8016 (t70) REVERT: R 367 ASP cc_start: 0.7948 (t0) cc_final: 0.7593 (t0) REVERT: A 405 PHE cc_start: 0.3882 (t80) cc_final: 0.3657 (t80) REVERT: C 553 ASP cc_start: 0.7440 (m-30) cc_final: 0.7206 (m-30) REVERT: D 382 TRP cc_start: 0.5733 (m100) cc_final: 0.5519 (m100) REVERT: E 364 LYS cc_start: 0.7709 (mttt) cc_final: 0.7241 (mtpp) REVERT: E 553 ASP cc_start: 0.7985 (p0) cc_final: 0.7689 (p0) REVERT: F 491 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7485 (ptp-110) REVERT: F 568 MET cc_start: 0.6889 (mmp) cc_final: 0.6599 (mmm) REVERT: H 453 ASP cc_start: 0.7214 (p0) cc_final: 0.6848 (p0) outliers start: 3 outliers final: 1 residues processed: 439 average time/residue: 0.1304 time to fit residues: 91.1880 Evaluate side-chains 317 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0030 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 231 GLN R 295 GLN R 365 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN D 385 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN K 518 HIS K 545 ASN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.138864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095641 restraints weight = 49219.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098660 restraints weight = 25928.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100564 restraints weight = 18114.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101649 restraints weight = 14770.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102166 restraints weight = 13192.297| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21361 Z= 0.245 Angle : 0.702 12.309 29211 Z= 0.361 Chirality : 0.050 0.554 3415 Planarity : 0.005 0.059 3716 Dihedral : 4.774 28.417 2832 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.31 % Allowed : 11.13 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2600 helix: -0.15 (0.24), residues: 462 sheet: 0.53 (0.18), residues: 825 loop : -0.54 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 57 TYR 0.021 0.002 TYR L 562 PHE 0.025 0.003 PHE H 516 TRP 0.023 0.002 TRP R 354 HIS 0.010 0.002 HIS E 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (21326) covalent geometry : angle 0.68299 / 0.36 (29129) SS BOND : bond 0.00272 / 0.14 ( 23) SS BOND : angle 1.38577 / 0.92 ( 46) hydrogen bonds : bond 0.04404 / 2.88 ( 666) hydrogen bonds : angle 6.60723 / 4.80 ( 2013) link_BETA1-4 : bond 0.00540 / 0.36 ( 1) link_BETA1-4 : angle 1.07699 / 0.75 ( 3) link_NAG-ASN : bond 0.00913 / 0.60 ( 11) link_NAG-ASN : angle 4.62627 / 2.98 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 317 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8267 (mm-30) REVERT: R 278 HIS cc_start: 0.8338 (t-90) cc_final: 0.8038 (t70) REVERT: R 295 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7278 (tm130) REVERT: R 367 ASP cc_start: 0.7844 (t0) cc_final: 0.7434 (t0) REVERT: R 370 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8081 (tt0) REVERT: A 564 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7750 (p) REVERT: C 455 TYR cc_start: 0.7492 (m-80) cc_final: 0.7175 (m-10) REVERT: C 534 TYR cc_start: 0.8720 (m-80) cc_final: 0.8496 (m-10) REVERT: D 391 LYS cc_start: 0.8102 (tptp) cc_final: 0.7693 (tptp) REVERT: E 364 LYS cc_start: 0.7853 (mttt) cc_final: 0.7448 (mtpp) REVERT: E 483 ASP cc_start: 0.7150 (t70) cc_final: 0.6770 (t70) REVERT: E 553 ASP cc_start: 0.8162 (p0) cc_final: 0.7883 (p0) REVERT: E 555 SER cc_start: 0.7820 (m) cc_final: 0.7582 (m) REVERT: G 506 MET cc_start: 0.7810 (mpp) cc_final: 0.7527 (mpp) REVERT: H 453 ASP cc_start: 0.7501 (p0) cc_final: 0.7222 (p0) REVERT: K 493 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7784 (mm-40) outliers start: 31 outliers final: 18 residues processed: 334 average time/residue: 0.1200 time to fit residues: 64.7135 Evaluate side-chains 289 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 117 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 242 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 295 GLN A 545 ASN B 385 GLN C 487 GLN D 393 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.138628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096827 restraints weight = 48894.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.099155 restraints weight = 28029.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.100517 restraints weight = 18631.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100925 restraints weight = 17838.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.100850 restraints weight = 15847.991| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21361 Z= 0.161 Angle : 0.616 10.353 29211 Z= 0.312 Chirality : 0.047 0.485 3415 Planarity : 0.004 0.056 3716 Dihedral : 4.525 27.905 2830 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.12 % Allowed : 12.95 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2600 helix: 0.03 (0.23), residues: 471 sheet: 0.47 (0.18), residues: 808 loop : -0.54 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 491 TYR 0.020 0.002 TYR L 562 PHE 0.024 0.002 PHE R 117 TRP 0.018 0.001 TRP R 268 HIS 0.011 0.001 HIS E 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (21326) covalent geometry : angle 0.59591 / 0.31 (29129) SS BOND : bond 0.00277 / 0.16 ( 23) SS BOND : angle 1.05520 / 0.69 ( 46) hydrogen bonds : bond 0.03853 / 2.56 ( 666) hydrogen bonds : angle 5.98913 / 4.38 ( 2013) link_BETA1-4 : bond 0.00484 / 0.32 ( 1) link_BETA1-4 : angle 1.07908 / 0.82 ( 3) link_NAG-ASN : bond 0.00947 / 0.62 ( 11) link_NAG-ASN : angle 4.58315 / 3.04 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8370 (mm-30) REVERT: R 278 HIS cc_start: 0.8664 (t-90) cc_final: 0.8144 (t-90) REVERT: R 295 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: R 367 ASP cc_start: 0.7966 (t0) cc_final: 0.7535 (t0) REVERT: R 370 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8070 (tt0) REVERT: R 375 LYS cc_start: 0.8047 (pptt) cc_final: 0.7838 (tmmt) REVERT: A 545 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8369 (t0) REVERT: C 455 TYR cc_start: 0.7491 (m-80) cc_final: 0.7176 (m-10) REVERT: C 534 TYR cc_start: 0.8675 (m-80) cc_final: 0.8460 (m-10) REVERT: D 499 LYS cc_start: 0.8885 (tppt) cc_final: 0.8667 (tptt) REVERT: E 364 LYS cc_start: 0.7867 (mttt) cc_final: 0.7361 (mtpp) REVERT: E 483 ASP cc_start: 0.7075 (t0) cc_final: 0.6644 (t70) REVERT: E 553 ASP cc_start: 0.8278 (p0) cc_final: 0.8020 (p0) REVERT: F 391 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7737 (tmtt) REVERT: G 419 ASN cc_start: 0.9011 (m-40) cc_final: 0.8797 (m110) REVERT: H 453 ASP cc_start: 0.7617 (p0) cc_final: 0.7352 (p0) REVERT: K 493 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7783 (mm-40) REVERT: K 534 TYR cc_start: 0.8101 (m-80) cc_final: 0.7751 (m-80) REVERT: L 455 TYR cc_start: 0.5828 (m-80) cc_final: 0.5288 (m-80) REVERT: L 488 TRP cc_start: 0.8179 (m100) cc_final: 0.7954 (m100) REVERT: J 46 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7782 (mtm-85) outliers start: 50 outliers final: 24 residues processed: 341 average time/residue: 0.1176 time to fit residues: 64.7665 Evaluate side-chains 301 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 28 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 233 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 116 ASN R 199 HIS R 263 ASN R 295 GLN A 545 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 439 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.133200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089814 restraints weight = 49157.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092424 restraints weight = 29458.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.092925 restraints weight = 19421.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093561 restraints weight = 19557.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093452 restraints weight = 17628.039| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 21361 Z= 0.340 Angle : 0.737 13.543 29211 Z= 0.379 Chirality : 0.050 0.470 3415 Planarity : 0.005 0.069 3716 Dihedral : 5.026 27.879 2830 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.67 % Allowed : 16.46 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2600 helix: -0.19 (0.23), residues: 471 sheet: 0.21 (0.18), residues: 812 loop : -0.71 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 491 TYR 0.028 0.002 TYR L 562 PHE 0.026 0.003 PHE R 369 TRP 0.027 0.002 TRP R 354 HIS 0.013 0.002 HIS E 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.34 (21326) covalent geometry : angle 0.71824 / 0.37 (29129) SS BOND : bond 0.00427 / 0.22 ( 23) SS BOND : angle 1.17773 / 0.75 ( 46) hydrogen bonds : bond 0.04043 / 2.66 ( 666) hydrogen bonds : angle 6.23497 / 4.57 ( 2013) link_BETA1-4 : bond 0.00733 / 0.49 ( 1) link_BETA1-4 : angle 0.98131 / 0.61 ( 3) link_NAG-ASN : bond 0.00877 / 0.57 ( 11) link_NAG-ASN : angle 4.83158 / 3.34 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8441 (mm-30) REVERT: R 278 HIS cc_start: 0.8705 (t-90) cc_final: 0.8161 (t-90) REVERT: R 290 MET cc_start: 0.7948 (pmm) cc_final: 0.6808 (ptt) REVERT: R 291 ASP cc_start: 0.7625 (m-30) cc_final: 0.6713 (m-30) REVERT: R 367 ASP cc_start: 0.7940 (t0) cc_final: 0.7455 (t0) REVERT: R 370 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8239 (tt0) REVERT: R 375 LYS cc_start: 0.8148 (pptt) cc_final: 0.7936 (tmmt) REVERT: A 545 ASN cc_start: 0.8797 (t160) cc_final: 0.8547 (t0) REVERT: C 455 TYR cc_start: 0.7818 (m-80) cc_final: 0.7554 (m-10) REVERT: C 465 ASN cc_start: 0.8950 (t0) cc_final: 0.8576 (t0) REVERT: D 368 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5401 (tp) REVERT: E 364 LYS cc_start: 0.7969 (mttt) cc_final: 0.7436 (mtpp) REVERT: E 483 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6626 (t70) REVERT: E 553 ASP cc_start: 0.8468 (p0) cc_final: 0.8152 (p0) REVERT: E 555 SER cc_start: 0.8043 (m) cc_final: 0.7808 (m) REVERT: F 493 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7802 (tm-30) REVERT: G 419 ASN cc_start: 0.9026 (m-40) cc_final: 0.8815 (m110) REVERT: H 453 ASP cc_start: 0.7774 (p0) cc_final: 0.7331 (p0) REVERT: K 493 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7994 (mm-40) REVERT: K 500 TYR cc_start: 0.8746 (p90) cc_final: 0.8441 (p90) REVERT: K 534 TYR cc_start: 0.8468 (m-80) cc_final: 0.7818 (m-80) REVERT: L 568 MET cc_start: 0.8560 (mmp) cc_final: 0.8331 (mmm) REVERT: J 46 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7812 (mtt-85) outliers start: 63 outliers final: 42 residues processed: 336 average time/residue: 0.1138 time to fit residues: 62.2936 Evaluate side-chains 304 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 225 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 295 GLN A 510 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.4179 r_free = 0.4179 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091552 restraints weight = 48539.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094543 restraints weight = 26670.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096373 restraints weight = 19052.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097498 restraints weight = 15793.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097952 restraints weight = 14186.304| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21361 Z= 0.162 Angle : 0.625 12.641 29211 Z= 0.317 Chirality : 0.047 0.438 3415 Planarity : 0.004 0.056 3716 Dihedral : 4.709 27.226 2830 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.54 % Allowed : 17.86 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2600 helix: -0.01 (0.23), residues: 478 sheet: 0.24 (0.18), residues: 821 loop : -0.57 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 491 TYR 0.020 0.002 TYR L 562 PHE 0.030 0.002 PHE R 369 TRP 0.037 0.002 TRP R 172 HIS 0.009 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (21326) covalent geometry : angle 0.60457 / 0.31 (29129) SS BOND : bond 0.00233 / 0.12 ( 23) SS BOND : angle 0.89167 / 0.57 ( 46) hydrogen bonds : bond 0.03496 / 2.34 ( 666) hydrogen bonds : angle 5.74144 / 4.20 ( 2013) link_BETA1-4 : bond 0.00751 / 0.50 ( 1) link_BETA1-4 : angle 0.84870 / 0.62 ( 3) link_NAG-ASN : bond 0.00717 / 0.45 ( 11) link_NAG-ASN : angle 4.68210 / 3.23 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 0.506 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. REVERT: R 192 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8255 (mm-30) REVERT: R 290 MET cc_start: 0.7678 (pmm) cc_final: 0.6838 (ptt) REVERT: R 291 ASP cc_start: 0.7161 (m-30) cc_final: 0.6671 (m-30) REVERT: R 367 ASP cc_start: 0.7690 (t0) cc_final: 0.7242 (t0) REVERT: R 370 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8166 (tt0) REVERT: R 375 LYS cc_start: 0.8052 (pptt) cc_final: 0.7844 (tmmt) REVERT: A 574 THR cc_start: 0.5976 (m) cc_final: 0.5664 (p) REVERT: C 455 TYR cc_start: 0.7792 (m-80) cc_final: 0.7535 (m-10) REVERT: C 510 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8069 (mm-40) REVERT: D 368 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.5170 (tp) REVERT: E 364 LYS cc_start: 0.8052 (mttt) cc_final: 0.7505 (mtpp) REVERT: E 483 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6633 (t70) REVERT: E 553 ASP cc_start: 0.8361 (p0) cc_final: 0.8060 (p0) REVERT: F 391 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7497 (tmtt) REVERT: F 493 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7924 (tm-30) REVERT: G 405 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4286 (t80) REVERT: G 419 ASN cc_start: 0.9037 (m-40) cc_final: 0.8789 (m110) REVERT: H 453 ASP cc_start: 0.7631 (p0) cc_final: 0.7288 (p0) REVERT: H 463 GLN cc_start: 0.8515 (tt0) cc_final: 0.8271 (tt0) REVERT: K 493 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7798 (mm-40) REVERT: K 500 TYR cc_start: 0.8602 (p90) cc_final: 0.8340 (p90) REVERT: K 534 TYR cc_start: 0.8334 (m-80) cc_final: 0.7782 (m-80) REVERT: L 488 TRP cc_start: 0.8286 (m100) cc_final: 0.7887 (m100) REVERT: J 46 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7670 (mtt-85) outliers start: 60 outliers final: 35 residues processed: 344 average time/residue: 0.1182 time to fit residues: 66.3047 Evaluate side-chains 309 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 188 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 116 ASN A 393 HIS A 510 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.136865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093030 restraints weight = 48672.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096053 restraints weight = 26544.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097857 restraints weight = 18921.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099003 restraints weight = 15663.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099510 restraints weight = 14071.841| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21361 Z= 0.129 Angle : 0.608 12.369 29211 Z= 0.305 Chirality : 0.046 0.403 3415 Planarity : 0.004 0.057 3716 Dihedral : 4.580 33.243 2830 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.62 % Allowed : 18.66 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2600 helix: 0.12 (0.23), residues: 476 sheet: 0.26 (0.18), residues: 811 loop : -0.51 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 491 TYR 0.023 0.002 TYR A 455 PHE 0.025 0.002 PHE R 369 TRP 0.048 0.002 TRP R 172 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21326) covalent geometry : angle 0.58780 / 0.30 (29129) SS BOND : bond 0.00472 / 0.18 ( 23) SS BOND : angle 1.10562 / 0.74 ( 46) hydrogen bonds : bond 0.03285 / 2.21 ( 666) hydrogen bonds : angle 5.45775 / 3.99 ( 2013) link_BETA1-4 : bond 0.00763 / 0.51 ( 1) link_BETA1-4 : angle 0.96521 / 0.74 ( 3) link_NAG-ASN : bond 0.00723 / 0.46 ( 11) link_NAG-ASN : angle 4.53606 / 3.13 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 0.608 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 117 PHE cc_start: 0.6989 (t80) cc_final: 0.6771 (t80) REVERT: R 192 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8213 (mm-30) REVERT: R 290 MET cc_start: 0.7773 (pmm) cc_final: 0.7068 (ptt) REVERT: R 293 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8668 (pt) REVERT: R 367 ASP cc_start: 0.7624 (t0) cc_final: 0.7205 (t0) REVERT: R 370 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8096 (tt0) REVERT: R 375 LYS cc_start: 0.8052 (pptt) cc_final: 0.7793 (tmmt) REVERT: B 416 ASP cc_start: 0.8476 (p0) cc_final: 0.8205 (t0) REVERT: C 455 TYR cc_start: 0.7714 (m-80) cc_final: 0.7463 (m-10) REVERT: D 368 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.5195 (tp) REVERT: D 562 TYR cc_start: 0.8573 (m-80) cc_final: 0.8280 (m-80) REVERT: E 364 LYS cc_start: 0.8154 (mttt) cc_final: 0.7553 (mtpp) REVERT: E 553 ASP cc_start: 0.8354 (p0) cc_final: 0.8039 (p0) REVERT: F 391 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7521 (tmtt) REVERT: F 493 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7953 (tm-30) REVERT: G 405 PHE cc_start: 0.5297 (OUTLIER) cc_final: 0.4371 (t80) REVERT: G 419 ASN cc_start: 0.9033 (m-40) cc_final: 0.8763 (m110) REVERT: H 453 ASP cc_start: 0.7693 (p0) cc_final: 0.7376 (p0) REVERT: K 500 TYR cc_start: 0.8569 (p90) cc_final: 0.8295 (p90) REVERT: K 534 TYR cc_start: 0.8177 (m-80) cc_final: 0.7690 (m-80) REVERT: L 455 TYR cc_start: 0.5698 (m-80) cc_final: 0.5133 (m-80) REVERT: L 488 TRP cc_start: 0.8207 (m100) cc_final: 0.7914 (m100) REVERT: J 46 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7627 (mtt-85) outliers start: 62 outliers final: 41 residues processed: 349 average time/residue: 0.1135 time to fit residues: 64.7671 Evaluate side-chains 327 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 120 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 249 optimal weight: 0.6980 chunk 220 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 100 optimal weight: 40.0000 chunk 138 optimal weight: 0.8980 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN D 385 GLN H 463 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.136043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090094 restraints weight = 48868.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093132 restraints weight = 26477.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095002 restraints weight = 18798.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096101 restraints weight = 15539.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096690 restraints weight = 13956.795| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21361 Z= 0.197 Angle : 0.635 12.385 29211 Z= 0.321 Chirality : 0.047 0.403 3415 Planarity : 0.004 0.056 3716 Dihedral : 4.651 30.983 2830 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.75 % Allowed : 19.68 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2600 helix: 0.24 (0.23), residues: 471 sheet: 0.20 (0.18), residues: 813 loop : -0.53 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 491 TYR 0.023 0.002 TYR E 455 PHE 0.020 0.002 PHE R 369 TRP 0.031 0.002 TRP R 362 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (21326) covalent geometry : angle 0.61673 / 0.32 (29129) SS BOND : bond 0.00293 / 0.14 ( 23) SS BOND : angle 0.91107 / 0.58 ( 46) hydrogen bonds : bond 0.03351 / 2.25 ( 666) hydrogen bonds : angle 5.52955 / 4.05 ( 2013) link_BETA1-4 : bond 0.00534 / 0.36 ( 1) link_BETA1-4 : angle 0.88453 / 0.64 ( 3) link_NAG-ASN : bond 0.00686 / 0.44 ( 11) link_NAG-ASN : angle 4.48234 / 3.08 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 292 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8351 (mm-30) REVERT: R 290 MET cc_start: 0.7803 (pmm) cc_final: 0.7098 (ptp) REVERT: R 291 ASP cc_start: 0.7529 (m-30) cc_final: 0.6982 (m-30) REVERT: R 367 ASP cc_start: 0.7729 (t0) cc_final: 0.7316 (t0) REVERT: R 370 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8185 (tt0) REVERT: R 375 LYS cc_start: 0.8110 (pptt) cc_final: 0.7863 (tmmt) REVERT: B 415 GLU cc_start: 0.7934 (mp0) cc_final: 0.7538 (tm-30) REVERT: B 416 ASP cc_start: 0.8536 (p0) cc_final: 0.7937 (p0) REVERT: C 455 TYR cc_start: 0.7802 (m-80) cc_final: 0.7584 (m-10) REVERT: D 368 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5188 (tp) REVERT: D 562 TYR cc_start: 0.8601 (m-80) cc_final: 0.8314 (m-80) REVERT: E 364 LYS cc_start: 0.8146 (mttt) cc_final: 0.7564 (mtpp) REVERT: E 553 ASP cc_start: 0.8437 (p0) cc_final: 0.8023 (p0) REVERT: F 485 PHE cc_start: 0.8707 (t80) cc_final: 0.8427 (t80) REVERT: F 493 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7991 (tm-30) REVERT: G 405 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4245 (t80) REVERT: G 419 ASN cc_start: 0.9036 (m-40) cc_final: 0.8778 (m110) REVERT: H 453 ASP cc_start: 0.7699 (p0) cc_final: 0.7259 (p0) REVERT: K 500 TYR cc_start: 0.8674 (p90) cc_final: 0.8361 (p90) REVERT: K 534 TYR cc_start: 0.8355 (m-80) cc_final: 0.7760 (m-80) REVERT: L 488 TRP cc_start: 0.8386 (m100) cc_final: 0.7972 (m100) REVERT: L 553 ASP cc_start: 0.7723 (t70) cc_final: 0.7468 (t0) REVERT: L 568 MET cc_start: 0.8434 (mmp) cc_final: 0.8233 (mmm) REVERT: J 46 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7585 (mtt-85) outliers start: 65 outliers final: 50 residues processed: 342 average time/residue: 0.1072 time to fit residues: 59.6179 Evaluate side-chains 327 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 385 GLN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 192 optimal weight: 8.9990 chunk 88 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 186 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 154 optimal weight: 0.0770 chunk 132 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 168 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 545 ASN C 487 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 GLN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.141542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102931 restraints weight = 48249.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.104343 restraints weight = 27280.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104159 restraints weight = 19922.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104663 restraints weight = 20811.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.104843 restraints weight = 18466.731| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21361 Z= 0.115 Angle : 0.620 11.701 29211 Z= 0.308 Chirality : 0.046 0.377 3415 Planarity : 0.004 0.071 3716 Dihedral : 4.492 28.943 2830 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.16 % Allowed : 20.48 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2600 helix: 0.26 (0.23), residues: 474 sheet: 0.36 (0.18), residues: 806 loop : -0.45 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 491 TYR 0.021 0.002 TYR E 455 PHE 0.032 0.002 PHE R 117 TRP 0.041 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (21326) covalent geometry : angle 0.60292 / 0.30 (29129) SS BOND : bond 0.00187 / 0.11 ( 23) SS BOND : angle 0.63319 / 0.40 ( 46) hydrogen bonds : bond 0.03132 / 2.11 ( 666) hydrogen bonds : angle 5.21833 / 3.82 ( 2013) link_BETA1-4 : bond 0.00917 / 0.61 ( 1) link_BETA1-4 : angle 0.96316 / 0.77 ( 3) link_NAG-ASN : bond 0.00781 / 0.50 ( 11) link_NAG-ASN : angle 4.33001 / 2.99 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 0.823 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8288 (mm-30) REVERT: R 290 MET cc_start: 0.7607 (pmm) cc_final: 0.6956 (ptt) REVERT: R 291 ASP cc_start: 0.7055 (m-30) cc_final: 0.6768 (m-30) REVERT: R 367 ASP cc_start: 0.7496 (t0) cc_final: 0.7224 (t0) REVERT: R 370 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8117 (tt0) REVERT: R 375 LYS cc_start: 0.8150 (pptt) cc_final: 0.7854 (tmmt) REVERT: C 358 PHE cc_start: 0.7859 (t80) cc_final: 0.7644 (t80) REVERT: D 419 ASN cc_start: 0.8768 (m110) cc_final: 0.8521 (m110) REVERT: D 562 TYR cc_start: 0.8423 (m-80) cc_final: 0.8187 (m-80) REVERT: E 364 LYS cc_start: 0.8121 (mttt) cc_final: 0.7501 (mtpp) REVERT: E 553 ASP cc_start: 0.8266 (p0) cc_final: 0.7951 (p0) REVERT: F 391 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7570 (tmtt) REVERT: F 493 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 405 PHE cc_start: 0.5123 (t80) cc_final: 0.4224 (t80) REVERT: G 419 ASN cc_start: 0.9064 (m-40) cc_final: 0.8795 (m110) REVERT: H 453 ASP cc_start: 0.7601 (p0) cc_final: 0.7319 (p0) REVERT: K 500 TYR cc_start: 0.8520 (p90) cc_final: 0.8277 (p90) REVERT: K 534 TYR cc_start: 0.8080 (m-80) cc_final: 0.7609 (m-80) REVERT: L 378 VAL cc_start: 0.1662 (OUTLIER) cc_final: 0.1183 (p) REVERT: L 488 TRP cc_start: 0.8313 (m100) cc_final: 0.7925 (m100) REVERT: L 553 ASP cc_start: 0.7786 (t70) cc_final: 0.7552 (t0) REVERT: L 568 MET cc_start: 0.8149 (mmp) cc_final: 0.7914 (mmm) REVERT: J 46 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7547 (mtt-85) outliers start: 51 outliers final: 36 residues processed: 357 average time/residue: 0.1199 time to fit residues: 69.9581 Evaluate side-chains 325 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 348 LEU Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 250 optimal weight: 0.2980 chunk 188 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 263 ASN R 295 GLN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.137317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097366 restraints weight = 48652.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098532 restraints weight = 29614.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098322 restraints weight = 21696.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098762 restraints weight = 21804.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098878 restraints weight = 20586.628| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21361 Z= 0.208 Angle : 0.652 12.018 29211 Z= 0.327 Chirality : 0.047 0.400 3415 Planarity : 0.004 0.058 3716 Dihedral : 4.603 28.207 2830 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.20 % Allowed : 21.12 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2600 helix: 0.31 (0.24), residues: 468 sheet: 0.29 (0.18), residues: 809 loop : -0.51 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 491 TYR 0.021 0.002 TYR C 455 PHE 0.034 0.002 PHE G 485 TRP 0.040 0.002 TRP R 362 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (21326) covalent geometry : angle 0.63564 / 0.32 (29129) SS BOND : bond 0.00262 / 0.14 ( 23) SS BOND : angle 0.79045 / 0.50 ( 46) hydrogen bonds : bond 0.03279 / 2.19 ( 666) hydrogen bonds : angle 5.41603 / 3.97 ( 2013) link_BETA1-4 : bond 0.00499 / 0.33 ( 1) link_BETA1-4 : angle 0.91771 / 0.69 ( 3) link_NAG-ASN : bond 0.00714 / 0.46 ( 11) link_NAG-ASN : angle 4.36218 / 2.99 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 283 time to evaluate : 0.721 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8226 (mm-30) REVERT: R 290 MET cc_start: 0.7784 (pmm) cc_final: 0.7221 (ptt) REVERT: R 291 ASP cc_start: 0.7407 (m-30) cc_final: 0.6931 (m-30) REVERT: R 367 ASP cc_start: 0.7683 (t0) cc_final: 0.7306 (t0) REVERT: R 370 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8133 (tt0) REVERT: D 419 ASN cc_start: 0.8696 (m110) cc_final: 0.8462 (m110) REVERT: E 364 LYS cc_start: 0.8259 (mttt) cc_final: 0.7695 (mtpp) REVERT: E 553 ASP cc_start: 0.8299 (p0) cc_final: 0.7888 (p0) REVERT: F 391 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7666 (tmtt) REVERT: F 493 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 405 PHE cc_start: 0.4930 (t80) cc_final: 0.4123 (t80) REVERT: G 419 ASN cc_start: 0.9016 (m-40) cc_final: 0.8751 (m110) REVERT: H 453 ASP cc_start: 0.7513 (p0) cc_final: 0.7202 (p0) REVERT: K 500 TYR cc_start: 0.8642 (p90) cc_final: 0.8355 (p90) REVERT: K 534 TYR cc_start: 0.8217 (m-80) cc_final: 0.7646 (m-80) REVERT: L 378 VAL cc_start: 0.1580 (OUTLIER) cc_final: 0.1120 (p) REVERT: L 488 TRP cc_start: 0.8483 (m100) cc_final: 0.7940 (m100) REVERT: L 553 ASP cc_start: 0.7844 (t70) cc_final: 0.7615 (t0) outliers start: 52 outliers final: 45 residues processed: 320 average time/residue: 0.1158 time to fit residues: 60.9817 Evaluate side-chains 318 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 230 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.0370 chunk 179 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS L 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.139507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101532 restraints weight = 48498.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.102122 restraints weight = 28308.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101923 restraints weight = 22179.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.102360 restraints weight = 21810.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102610 restraints weight = 19799.183| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21361 Z= 0.126 Angle : 0.634 11.590 29211 Z= 0.316 Chirality : 0.046 0.376 3415 Planarity : 0.005 0.109 3716 Dihedral : 4.534 27.694 2830 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 21.58 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2600 helix: 0.30 (0.24), residues: 467 sheet: 0.32 (0.18), residues: 793 loop : -0.46 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 491 TYR 0.020 0.002 TYR E 455 PHE 0.038 0.002 PHE G 485 TRP 0.042 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21326) covalent geometry : angle 0.61809 / 0.31 (29129) SS BOND : bond 0.00188 / 0.11 ( 23) SS BOND : angle 0.64947 / 0.41 ( 46) hydrogen bonds : bond 0.03139 / 2.11 ( 666) hydrogen bonds : angle 5.21338 / 3.81 ( 2013) link_BETA1-4 : bond 0.00450 / 0.30 ( 1) link_BETA1-4 : angle 0.86021 / 0.67 ( 3) link_NAG-ASN : bond 0.00699 / 0.44 ( 11) link_NAG-ASN : angle 4.29554 / 2.96 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 0.658 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: R 192 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8264 (mm-30) REVERT: R 290 MET cc_start: 0.7727 (pmm) cc_final: 0.7187 (ptt) REVERT: R 291 ASP cc_start: 0.7147 (m-30) cc_final: 0.6737 (m-30) REVERT: R 367 ASP cc_start: 0.7528 (t0) cc_final: 0.7260 (t0) REVERT: R 370 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8146 (tt0) REVERT: C 380 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3423 (mt) REVERT: D 419 ASN cc_start: 0.8689 (m110) cc_final: 0.8451 (m110) REVERT: E 364 LYS cc_start: 0.8164 (mttt) cc_final: 0.7587 (mtpp) REVERT: E 553 ASP cc_start: 0.8241 (p0) cc_final: 0.7872 (p0) REVERT: F 493 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8113 (tm-30) REVERT: G 405 PHE cc_start: 0.5029 (t80) cc_final: 0.4223 (t80) REVERT: G 419 ASN cc_start: 0.9027 (m-40) cc_final: 0.8762 (m110) REVERT: H 453 ASP cc_start: 0.7565 (p0) cc_final: 0.7274 (p0) REVERT: K 500 TYR cc_start: 0.8591 (p90) cc_final: 0.8317 (p90) REVERT: K 534 TYR cc_start: 0.8139 (m-80) cc_final: 0.7637 (m-80) REVERT: L 378 VAL cc_start: 0.1805 (OUTLIER) cc_final: 0.1326 (p) REVERT: L 488 TRP cc_start: 0.8389 (m100) cc_final: 0.7880 (m100) REVERT: L 553 ASP cc_start: 0.7680 (t70) cc_final: 0.7390 (t0) outliers start: 47 outliers final: 42 residues processed: 326 average time/residue: 0.1194 time to fit residues: 64.1608 Evaluate side-chains 324 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 348 LEU Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 133 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 238 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 263 ASN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN F 400 HIS ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087009 restraints weight = 48815.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089839 restraints weight = 26975.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091552 restraints weight = 19400.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092627 restraints weight = 16134.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093132 restraints weight = 14524.484| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 21361 Z= 0.326 Angle : 0.744 12.032 29211 Z= 0.377 Chirality : 0.051 0.413 3415 Planarity : 0.005 0.097 3716 Dihedral : 4.998 29.722 2830 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.41 % Allowed : 21.20 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2600 helix: -0.03 (0.23), residues: 473 sheet: 0.02 (0.18), residues: 800 loop : -0.63 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 491 TYR 0.029 0.003 TYR E 455 PHE 0.032 0.003 PHE G 485 TRP 0.043 0.003 TRP R 362 HIS 0.009 0.002 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.33 (21326) covalent geometry : angle 0.72840 / 0.37 (29129) SS BOND : bond 0.00401 / 0.22 ( 23) SS BOND : angle 1.06159 / 0.67 ( 46) hydrogen bonds : bond 0.03660 / 2.42 ( 666) hydrogen bonds : angle 5.80156 / 4.25 ( 2013) link_BETA1-4 : bond 0.00252 / 0.17 ( 1) link_BETA1-4 : angle 0.84347 / 0.55 ( 3) link_NAG-ASN : bond 0.00765 / 0.48 ( 11) link_NAG-ASN : angle 4.53829 / 3.07 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3506.84 seconds wall clock time: 61 minutes 41.64 seconds (3701.64 seconds total)