Starting phenix.real_space_refine on Thu Mar 5 09:10:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y09_33538/03_2026/7y09_33538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y09_33538/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y09_33538/03_2026/7y09_33538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y09_33538/03_2026/7y09_33538.map" model { file = "/net/cci-nas-00/data/ceres_data/7y09_33538/03_2026/7y09_33538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y09_33538/03_2026/7y09_33538.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.61, per 1000 atoms: 0.27 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: 1.66 Conformation dependent library (CDL) restraints added in 943.9 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: 0.97 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: 3.95 Time building geometry restraints manager: 2.30 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 - 20.27: 12112 20.27 - 40.53: 849 40.53 - 60.80: 116 60.80 - 81.06: 41 81.06 - 101.33: 9 Dihedral angle restraints: 13127 sinusoidal: 5372 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 13124 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: 3.130 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.610 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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 : 14.295 101.328 7998 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 covalent geometry : bond 0.00306 (21326) covalent geometry : angle 0.67226 (29129) SS BOND : bond 0.00164 ( 23) SS BOND : angle 1.29201 ( 46) hydrogen bonds : bond 0.25599 ( 666) hydrogen bonds : angle 9.86242 ( 2013) link_BETA1-4 : bond 0.00961 ( 1) link_BETA1-4 : angle 1.25793 ( 3) link_NAG-ASN : bond 0.01214 ( 11) link_NAG-ASN : angle 5.34192 ( 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 : 0.802 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: 0.1411 time to fit residues: 98.6298 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 : 0.810 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 C 487 GLN D 385 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.138448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.095475 restraints weight = 49257.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098685 restraints weight = 28449.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100755 restraints weight = 18368.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100631 restraints weight = 16214.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100783 restraints weight = 15482.156| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21361 Z= 0.254 Angle : 0.701 12.293 29211 Z= 0.361 Chirality : 0.050 0.578 3415 Planarity : 0.005 0.059 3716 Dihedral : 7.358 87.228 3084 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 11.09 % 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: -0.22 (0.16), residues: 2600 helix: -0.09 (0.24), residues: 462 sheet: 0.52 (0.18), residues: 834 loop : -0.54 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 443 TYR 0.021 0.002 TYR L 562 PHE 0.023 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 covalent geometry : bond 0.00567 (21326) covalent geometry : angle 0.68110 (29129) SS BOND : bond 0.00271 ( 23) SS BOND : angle 1.35784 ( 46) hydrogen bonds : bond 0.04265 ( 666) hydrogen bonds : angle 6.61406 ( 2013) link_BETA1-4 : bond 0.00505 ( 1) link_BETA1-4 : angle 1.93177 ( 3) link_NAG-ASN : bond 0.00942 ( 11) link_NAG-ASN : angle 4.69157 ( 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 349 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 317 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8360 (mm-30) REVERT: R 278 HIS cc_start: 0.8560 (t-90) cc_final: 0.8145 (t70) REVERT: R 295 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7104 (tp-100) REVERT: R 367 ASP cc_start: 0.7949 (t0) cc_final: 0.7541 (t0) REVERT: R 370 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8101 (tt0) REVERT: A 564 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7747 (p) REVERT: C 455 TYR cc_start: 0.7449 (m-80) cc_final: 0.7171 (m-10) REVERT: C 534 TYR cc_start: 0.8662 (m-80) cc_final: 0.8441 (m-10) REVERT: D 391 LYS cc_start: 0.8144 (tptp) cc_final: 0.7715 (tptp) REVERT: E 364 LYS cc_start: 0.7816 (mttt) cc_final: 0.7399 (mtpp) REVERT: E 483 ASP cc_start: 0.7092 (t70) cc_final: 0.6732 (t70) REVERT: E 553 ASP cc_start: 0.8166 (p0) cc_final: 0.7897 (p0) REVERT: E 555 SER cc_start: 0.7800 (m) cc_final: 0.7566 (m) REVERT: G 506 MET cc_start: 0.7907 (mpp) cc_final: 0.7592 (mpp) REVERT: H 453 ASP cc_start: 0.7451 (p0) cc_final: 0.7206 (p0) REVERT: K 493 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7798 (mm-40) outliers start: 32 outliers final: 18 residues processed: 335 average time/residue: 0.1366 time to fit residues: 74.2877 Evaluate side-chains 292 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 515 TYR 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 K residue 484 VAL 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: 9.9990 chunk 136 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 186 optimal weight: 30.0000 chunk 242 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN D 393 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 385 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.139733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.096752 restraints weight = 48821.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099909 restraints weight = 25564.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101881 restraints weight = 17813.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.103018 restraints weight = 14551.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103535 restraints weight = 12981.845| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21361 Z= 0.132 Angle : 0.610 10.572 29211 Z= 0.307 Chirality : 0.047 0.502 3415 Planarity : 0.004 0.055 3716 Dihedral : 6.851 76.327 3082 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.90 % Allowed : 12.70 % Favored : 85.40 % 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 (0.16), residues: 2600 helix: 0.06 (0.23), residues: 471 sheet: 0.59 (0.18), residues: 816 loop : -0.54 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 491 TYR 0.019 0.002 TYR J 134 PHE 0.023 0.002 PHE R 117 TRP 0.017 0.001 TRP L 528 HIS 0.008 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00299 (21326) covalent geometry : angle 0.58938 (29129) SS BOND : bond 0.00224 ( 23) SS BOND : angle 0.96932 ( 46) hydrogen bonds : bond 0.03835 ( 666) hydrogen bonds : angle 5.98174 ( 2013) link_BETA1-4 : bond 0.01147 ( 1) link_BETA1-4 : angle 2.56967 ( 3) link_NAG-ASN : bond 0.00985 ( 11) link_NAG-ASN : angle 4.62216 ( 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 359 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8221 (mm-30) REVERT: R 278 HIS cc_start: 0.8372 (t-90) cc_final: 0.7991 (t-90) REVERT: R 295 GLN cc_start: 0.7481 (tm-30) cc_final: 0.6857 (tm-30) REVERT: R 367 ASP cc_start: 0.7791 (t0) cc_final: 0.7458 (t0) REVERT: R 370 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8064 (tt0) REVERT: A 545 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8411 (t0) REVERT: C 455 TYR cc_start: 0.7531 (m-80) cc_final: 0.7242 (m-10) REVERT: C 534 TYR cc_start: 0.8654 (m-80) cc_final: 0.8425 (m-10) REVERT: D 499 LYS cc_start: 0.8874 (tppt) cc_final: 0.8645 (tptt) REVERT: E 364 LYS cc_start: 0.7944 (mttt) cc_final: 0.7422 (mtpp) REVERT: E 483 ASP cc_start: 0.7087 (t0) cc_final: 0.6373 (t70) REVERT: E 553 ASP cc_start: 0.8133 (p0) cc_final: 0.7827 (p0) REVERT: F 391 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7573 (tmtt) REVERT: H 453 ASP cc_start: 0.7559 (p0) cc_final: 0.7305 (p0) REVERT: H 547 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8758 (t) REVERT: K 493 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7700 (mm-40) REVERT: K 534 TYR cc_start: 0.7987 (m-80) cc_final: 0.7694 (m-80) outliers start: 45 outliers final: 19 residues processed: 344 average time/residue: 0.1324 time to fit residues: 72.9238 Evaluate side-chains 307 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 391 LYS Chi-restraints excluded: chain G residue 405 PHE 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 L residue 350 ILE Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE 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: 0.9990 chunk 171 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 233 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 ASN R 295 GLN A 545 ASN B 385 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS F 510 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.090752 restraints weight = 49036.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093700 restraints weight = 27036.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095372 restraints weight = 19397.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096542 restraints weight = 16146.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097030 restraints weight = 14552.547| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21361 Z= 0.264 Angle : 0.684 12.872 29211 Z= 0.349 Chirality : 0.049 0.481 3415 Planarity : 0.005 0.057 3716 Dihedral : 6.673 67.928 3082 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.41 % Allowed : 15.53 % Favored : 82.06 % 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: -0.32 (0.16), residues: 2600 helix: 0.02 (0.23), residues: 471 sheet: 0.32 (0.18), residues: 819 loop : -0.57 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 491 TYR 0.025 0.002 TYR L 562 PHE 0.019 0.002 PHE D 358 TRP 0.026 0.002 TRP R 354 HIS 0.011 0.002 HIS E 518 Details of bonding type rmsd covalent geometry : bond 0.00606 (21326) covalent geometry : angle 0.66358 (29129) SS BOND : bond 0.00349 ( 23) SS BOND : angle 1.14494 ( 46) hydrogen bonds : bond 0.03746 ( 666) hydrogen bonds : angle 5.97419 ( 2013) link_BETA1-4 : bond 0.00935 ( 1) link_BETA1-4 : angle 2.52757 ( 3) link_NAG-ASN : bond 0.00924 ( 11) link_NAG-ASN : angle 4.77130 ( 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 357 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8270 (mm-30) REVERT: R 278 HIS cc_start: 0.8393 (t-90) cc_final: 0.8020 (t-90) REVERT: R 290 MET cc_start: 0.7865 (pmm) cc_final: 0.6551 (ptt) REVERT: R 295 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7072 (tp-100) REVERT: R 367 ASP cc_start: 0.7794 (t0) cc_final: 0.7337 (t0) REVERT: R 370 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8114 (tt0) REVERT: R 375 LYS cc_start: 0.7866 (pptt) cc_final: 0.7624 (tmmt) REVERT: A 545 ASN cc_start: 0.8774 (t160) cc_final: 0.8503 (t0) REVERT: B 354 PHE cc_start: 0.8372 (t80) cc_final: 0.8119 (t80) REVERT: C 455 TYR cc_start: 0.7757 (m-80) cc_final: 0.7509 (m-10) REVERT: C 465 ASN cc_start: 0.8904 (t0) cc_final: 0.8540 (t0) REVERT: C 510 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7977 (mm-40) REVERT: D 368 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.5005 (tp) REVERT: E 364 LYS cc_start: 0.8079 (mttt) cc_final: 0.7535 (mtpp) REVERT: E 483 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6411 (t70) REVERT: E 553 ASP cc_start: 0.8370 (p0) cc_final: 0.8064 (p0) REVERT: F 463 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8641 (mm110) REVERT: F 489 MET cc_start: 0.8895 (mmp) cc_final: 0.8691 (mmm) REVERT: H 453 ASP cc_start: 0.7645 (p0) cc_final: 0.7284 (p0) REVERT: H 463 GLN cc_start: 0.8504 (tt0) cc_final: 0.8257 (tt0) REVERT: K 500 TYR cc_start: 0.8601 (p90) cc_final: 0.8363 (p90) REVERT: K 534 TYR cc_start: 0.8296 (m-80) cc_final: 0.7766 (m-80) REVERT: L 545 ASN cc_start: 0.7878 (t160) cc_final: 0.7629 (t0) REVERT: L 568 MET cc_start: 0.8474 (mmp) cc_final: 0.8226 (mmm) outliers start: 57 outliers final: 39 residues processed: 340 average time/residue: 0.1323 time to fit residues: 72.8471 Evaluate side-chains 309 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 376 TYR 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 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 522 THR 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 463 GLN 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 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 H residue 567 VAL 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 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 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: 2.9990 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 225 optimal weight: 0.8980 chunk 211 optimal weight: 20.0000 chunk 242 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN B 545 ASN ** K 385 GLN ** 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 = 0.4195 r_free = 0.4195 target = 0.136923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092982 restraints weight = 48482.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095994 restraints weight = 26418.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097878 restraints weight = 18839.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098865 restraints weight = 15556.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099534 restraints weight = 14033.669| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21361 Z= 0.148 Angle : 0.615 12.549 29211 Z= 0.309 Chirality : 0.047 0.437 3415 Planarity : 0.004 0.057 3716 Dihedral : 6.222 61.613 3082 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.37 % Allowed : 17.31 % Favored : 80.32 % 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: -0.27 (0.16), residues: 2600 helix: 0.11 (0.23), residues: 472 sheet: 0.25 (0.18), residues: 840 loop : -0.48 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 491 TYR 0.020 0.002 TYR L 562 PHE 0.017 0.002 PHE R 117 TRP 0.031 0.002 TRP R 172 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00336 (21326) covalent geometry : angle 0.59379 (29129) SS BOND : bond 0.00199 ( 23) SS BOND : angle 0.96219 ( 46) hydrogen bonds : bond 0.03418 ( 666) hydrogen bonds : angle 5.60510 ( 2013) link_BETA1-4 : bond 0.01163 ( 1) link_BETA1-4 : angle 2.78804 ( 3) link_NAG-ASN : bond 0.00760 ( 11) link_NAG-ASN : angle 4.66660 ( 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 361 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8224 (mm-30) REVERT: R 272 MET cc_start: 0.7702 (mmm) cc_final: 0.7121 (mmm) REVERT: R 290 MET cc_start: 0.7788 (pmm) cc_final: 0.6634 (ptt) REVERT: R 293 ILE cc_start: 0.8801 (pt) cc_final: 0.8576 (pt) REVERT: R 295 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: R 367 ASP cc_start: 0.7712 (t0) cc_final: 0.7247 (t0) REVERT: R 370 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8118 (tt0) REVERT: R 375 LYS cc_start: 0.7956 (pptt) cc_final: 0.7687 (tmmt) REVERT: C 455 TYR cc_start: 0.7737 (m-80) cc_final: 0.7446 (m-10) REVERT: D 368 LEU cc_start: 0.5135 (OUTLIER) cc_final: 0.4894 (tp) REVERT: E 364 LYS cc_start: 0.8111 (mttt) cc_final: 0.7525 (mtpp) REVERT: E 553 ASP cc_start: 0.8328 (p0) cc_final: 0.8018 (p0) REVERT: F 391 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7437 (tmtt) REVERT: F 489 MET cc_start: 0.8943 (mmp) cc_final: 0.8721 (mmm) REVERT: F 493 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7815 (tm-30) REVERT: G 405 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4136 (t80) REVERT: H 453 ASP cc_start: 0.7604 (p0) cc_final: 0.7274 (p0) REVERT: H 463 GLN cc_start: 0.8467 (tt0) cc_final: 0.8242 (tt0) REVERT: K 534 TYR cc_start: 0.8182 (m-80) cc_final: 0.7708 (m-80) REVERT: L 455 TYR cc_start: 0.5707 (m-80) cc_final: 0.5184 (m-80) outliers start: 56 outliers final: 36 residues processed: 345 average time/residue: 0.1285 time to fit residues: 73.0947 Evaluate side-chains 321 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 555 SER 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 D residue 363 THR Chi-restraints excluded: chain D residue 368 LEU 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 483 ASP Chi-restraints excluded: chain F residue 391 LYS 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 518 HIS Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 567 VAL 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 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 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: 20.0000 chunk 220 optimal weight: 0.0020 chunk 149 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 1 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 ASN R 295 GLN A 393 HIS ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN C 490 GLN D 385 GLN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 385 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.138581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.095398 restraints weight = 48715.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098995 restraints weight = 28003.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.100257 restraints weight = 18102.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100465 restraints weight = 16299.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100769 restraints weight = 15617.228| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21361 Z= 0.114 Angle : 0.610 12.361 29211 Z= 0.303 Chirality : 0.046 0.401 3415 Planarity : 0.004 0.062 3716 Dihedral : 5.823 57.732 3082 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.33 % Allowed : 17.94 % Favored : 79.73 % 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: -0.16 (0.17), residues: 2600 helix: 0.26 (0.24), residues: 476 sheet: 0.35 (0.18), residues: 814 loop : -0.46 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 491 TYR 0.020 0.002 TYR A 455 PHE 0.016 0.002 PHE D 358 TRP 0.030 0.001 TRP L 488 HIS 0.011 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00260 (21326) covalent geometry : angle 0.59012 (29129) SS BOND : bond 0.00210 ( 23) SS BOND : angle 0.80315 ( 46) hydrogen bonds : bond 0.03249 ( 666) hydrogen bonds : angle 5.33751 ( 2013) link_BETA1-4 : bond 0.01149 ( 1) link_BETA1-4 : angle 2.97801 ( 3) link_NAG-ASN : bond 0.00779 ( 11) link_NAG-ASN : angle 4.51270 ( 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 370 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 0.767 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: 0.7120 (t80) cc_final: 0.6910 (t80) REVERT: R 192 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8346 (mm-30) REVERT: R 272 MET cc_start: 0.7594 (mmm) cc_final: 0.7265 (mmm) REVERT: R 290 MET cc_start: 0.7610 (pmm) cc_final: 0.6695 (ptt) REVERT: R 291 ASP cc_start: 0.6860 (m-30) cc_final: 0.6521 (m-30) REVERT: R 293 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8446 (pt) REVERT: R 295 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7201 (tp-100) REVERT: R 303 TRP cc_start: 0.8944 (t60) cc_final: 0.8021 (t60) REVERT: R 367 ASP cc_start: 0.7805 (t0) cc_final: 0.7399 (t0) REVERT: R 370 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8100 (tt0) REVERT: R 375 LYS cc_start: 0.8140 (pptt) cc_final: 0.7818 (tmmt) REVERT: B 416 ASP cc_start: 0.8611 (p0) cc_final: 0.8319 (t0) REVERT: C 455 TYR cc_start: 0.7622 (m-80) cc_final: 0.7365 (m-10) REVERT: C 489 MET cc_start: 0.7781 (mtp) cc_final: 0.7543 (mtt) REVERT: D 368 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5086 (tp) REVERT: E 364 LYS cc_start: 0.7977 (mttt) cc_final: 0.7431 (mtpp) REVERT: E 553 ASP cc_start: 0.8352 (p0) cc_final: 0.8049 (p0) REVERT: F 391 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7517 (tmtt) REVERT: F 485 PHE cc_start: 0.8538 (t80) cc_final: 0.8253 (t80) REVERT: F 493 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7778 (tm-30) REVERT: G 405 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.4294 (t80) REVERT: H 453 ASP cc_start: 0.7661 (p0) cc_final: 0.7397 (p0) REVERT: K 534 TYR cc_start: 0.8082 (m-80) cc_final: 0.7622 (m-80) REVERT: L 568 MET cc_start: 0.8373 (mmp) cc_final: 0.8130 (mmm) outliers start: 55 outliers final: 35 residues processed: 350 average time/residue: 0.1276 time to fit residues: 73.6253 Evaluate side-chains 327 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 295 GLN 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 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 538 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 368 LEU Chi-restraints excluded: chain D residue 499 LYS Chi-restraints excluded: chain D residue 522 THR 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 405 PHE Chi-restraints excluded: chain G residue 518 HIS 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 H residue 567 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 516 PHE 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 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: 0.7980 chunk 25 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 164 optimal weight: 8.9990 chunk 249 optimal weight: 0.8980 chunk 220 optimal weight: 0.0170 chunk 62 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C 487 GLN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN ** K 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.138112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094500 restraints weight = 48732.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097550 restraints weight = 26426.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099404 restraints weight = 18747.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.100539 restraints weight = 15470.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101002 restraints weight = 13867.972| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21361 Z= 0.132 Angle : 0.606 12.442 29211 Z= 0.302 Chirality : 0.046 0.398 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.582 58.100 3082 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.33 % Allowed : 19.13 % Favored : 78.54 % 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: -0.06 (0.17), residues: 2600 helix: 0.37 (0.24), residues: 470 sheet: 0.42 (0.18), residues: 809 loop : -0.41 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 491 TYR 0.019 0.002 TYR A 455 PHE 0.021 0.002 PHE L 424 TRP 0.036 0.002 TRP R 299 HIS 0.011 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00307 (21326) covalent geometry : angle 0.58648 (29129) SS BOND : bond 0.00214 ( 23) SS BOND : angle 0.84151 ( 46) hydrogen bonds : bond 0.03164 ( 666) hydrogen bonds : angle 5.27421 ( 2013) link_BETA1-4 : bond 0.01302 ( 1) link_BETA1-4 : angle 3.03376 ( 3) link_NAG-ASN : bond 0.00733 ( 11) link_NAG-ASN : angle 4.41924 ( 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 354 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 0.806 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: 0.8521 (mm-30) cc_final: 0.8216 (mm-30) REVERT: R 272 MET cc_start: 0.7475 (mmm) cc_final: 0.7226 (mmm) REVERT: R 290 MET cc_start: 0.7610 (pmm) cc_final: 0.6993 (ptt) REVERT: R 293 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (pt) REVERT: R 303 TRP cc_start: 0.8963 (t60) cc_final: 0.8051 (t60) REVERT: R 367 ASP cc_start: 0.7629 (t0) cc_final: 0.7270 (t0) REVERT: R 370 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8054 (tt0) REVERT: R 375 LYS cc_start: 0.8024 (pptt) cc_final: 0.7680 (tmmt) REVERT: A 545 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8464 (t0) REVERT: C 455 TYR cc_start: 0.7695 (m-80) cc_final: 0.7416 (m-10) REVERT: D 368 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5106 (tp) REVERT: E 364 LYS cc_start: 0.8092 (mttt) cc_final: 0.7524 (mtpp) REVERT: E 553 ASP cc_start: 0.8333 (p0) cc_final: 0.8033 (p0) REVERT: F 489 MET cc_start: 0.8660 (mmp) cc_final: 0.8404 (mmm) REVERT: F 493 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7711 (tm-30) REVERT: G 405 PHE cc_start: 0.5078 (OUTLIER) cc_final: 0.4264 (t80) REVERT: H 453 ASP cc_start: 0.7704 (p0) cc_final: 0.7405 (p0) REVERT: K 534 TYR cc_start: 0.8069 (m-80) cc_final: 0.7617 (m-80) outliers start: 55 outliers final: 41 residues processed: 338 average time/residue: 0.1286 time to fit residues: 71.1369 Evaluate side-chains 332 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 293 ILE 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 360 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL 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 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 383 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 405 PHE Chi-restraints excluded: chain G residue 518 HIS 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 H residue 567 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 416 ASP 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 18 THR Chi-restraints excluded: chain J residue 37 ILE 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: 5.9990 chunk 88 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 186 optimal weight: 30.0000 chunk 3 optimal weight: 0.1980 chunk 154 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 385 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.144538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103346 restraints weight = 48374.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104837 restraints weight = 27430.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104881 restraints weight = 19367.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105518 restraints weight = 19017.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105632 restraints weight = 16536.396| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21361 Z= 0.113 Angle : 0.601 12.180 29211 Z= 0.298 Chirality : 0.046 0.395 3415 Planarity : 0.004 0.058 3716 Dihedral : 5.297 58.652 3082 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.16 % Allowed : 19.76 % Favored : 78.08 % 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: -0.04 (0.17), residues: 2600 helix: 0.40 (0.24), residues: 474 sheet: 0.45 (0.18), residues: 822 loop : -0.42 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 491 TYR 0.017 0.002 TYR A 455 PHE 0.035 0.001 PHE G 485 TRP 0.036 0.002 TRP R 362 HIS 0.012 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00260 (21326) covalent geometry : angle 0.58270 (29129) SS BOND : bond 0.00211 ( 23) SS BOND : angle 0.75151 ( 46) hydrogen bonds : bond 0.03067 ( 666) hydrogen bonds : angle 5.12909 ( 2013) link_BETA1-4 : bond 0.01270 ( 1) link_BETA1-4 : angle 3.08204 ( 3) link_NAG-ASN : bond 0.00750 ( 11) link_NAG-ASN : angle 4.32115 ( 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 361 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 0.836 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: 0.8568 (mm-30) cc_final: 0.8271 (mm-30) REVERT: R 290 MET cc_start: 0.7547 (pmm) cc_final: 0.6984 (ptt) REVERT: R 295 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6598 (tm-30) REVERT: R 303 TRP cc_start: 0.8906 (t60) cc_final: 0.8021 (t60) REVERT: R 367 ASP cc_start: 0.7565 (t0) cc_final: 0.7258 (t0) REVERT: R 370 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8061 (tt0) REVERT: R 375 LYS cc_start: 0.8121 (pptt) cc_final: 0.7727 (tmmt) REVERT: C 455 TYR cc_start: 0.7643 (m-80) cc_final: 0.7434 (m-10) REVERT: D 368 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.5079 (tp) REVERT: E 364 LYS cc_start: 0.8040 (mttt) cc_final: 0.7431 (mtpp) REVERT: E 500 TYR cc_start: 0.8331 (p90) cc_final: 0.8118 (p90) REVERT: E 553 ASP cc_start: 0.8306 (p0) cc_final: 0.8015 (p0) REVERT: F 489 MET cc_start: 0.8690 (mmp) cc_final: 0.8396 (mmm) REVERT: F 493 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7761 (tm-30) REVERT: G 405 PHE cc_start: 0.5130 (OUTLIER) cc_final: 0.4355 (t80) REVERT: G 488 TRP cc_start: 0.8437 (m100) cc_final: 0.8143 (m100) REVERT: K 534 TYR cc_start: 0.8055 (m-80) cc_final: 0.7636 (m-80) REVERT: L 378 VAL cc_start: 0.1310 (OUTLIER) cc_final: 0.0824 (p) REVERT: L 553 ASP cc_start: 0.7759 (t70) cc_final: 0.7461 (t0) outliers start: 51 outliers final: 39 residues processed: 346 average time/residue: 0.1305 time to fit residues: 73.8095 Evaluate side-chains 334 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 315 PHE 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 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 499 LYS 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 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 H residue 567 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 416 ASP 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 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 99 THR 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: 0.6980 chunk 188 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 116 optimal weight: 0.0270 chunk 239 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 chunk 204 optimal weight: 0.0980 chunk 42 optimal weight: 0.0770 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN A 545 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.146418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103854 restraints weight = 48758.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105705 restraints weight = 27154.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106306 restraints weight = 18756.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.106987 restraints weight = 18046.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.106930 restraints weight = 15399.465| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 21361 Z= 0.109 Angle : 0.604 11.949 29211 Z= 0.301 Chirality : 0.046 0.398 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.144 57.831 3082 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.99 % Allowed : 20.19 % Favored : 77.82 % 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: 0.05 (0.17), residues: 2600 helix: 0.49 (0.24), residues: 467 sheet: 0.56 (0.18), residues: 806 loop : -0.40 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 491 TYR 0.024 0.002 TYR R 296 PHE 0.030 0.001 PHE G 485 TRP 0.041 0.002 TRP R 362 HIS 0.013 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00246 (21326) covalent geometry : angle 0.58637 (29129) SS BOND : bond 0.00187 ( 23) SS BOND : angle 0.69899 ( 46) hydrogen bonds : bond 0.03108 ( 666) hydrogen bonds : angle 5.03895 ( 2013) link_BETA1-4 : bond 0.01250 ( 1) link_BETA1-4 : angle 3.10594 ( 3) link_NAG-ASN : bond 0.00761 ( 11) link_NAG-ASN : angle 4.22595 ( 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 353 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 0.750 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: 0.8712 (mm-30) cc_final: 0.8376 (mm-30) REVERT: R 290 MET cc_start: 0.7486 (pmm) cc_final: 0.7174 (ptt) REVERT: R 291 ASP cc_start: 0.6806 (m-30) cc_final: 0.6421 (m-30) REVERT: R 295 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: R 367 ASP cc_start: 0.7703 (t0) cc_final: 0.7384 (t0) REVERT: R 370 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8065 (tt0) REVERT: R 375 LYS cc_start: 0.8177 (pptt) cc_final: 0.7783 (tmmt) REVERT: A 441 ILE cc_start: 0.8403 (tp) cc_final: 0.8191 (tt) REVERT: C 455 TYR cc_start: 0.7531 (m-80) cc_final: 0.7301 (m-10) REVERT: D 368 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.5063 (tp) REVERT: E 364 LYS cc_start: 0.7883 (mttt) cc_final: 0.7298 (mtpp) REVERT: E 500 TYR cc_start: 0.8325 (p90) cc_final: 0.8123 (p90) REVERT: E 553 ASP cc_start: 0.8368 (p0) cc_final: 0.8109 (p0) REVERT: F 489 MET cc_start: 0.8746 (mmp) cc_final: 0.8352 (mmm) REVERT: F 493 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7837 (tm-30) REVERT: G 405 PHE cc_start: 0.5257 (OUTLIER) cc_final: 0.4441 (t80) REVERT: G 488 TRP cc_start: 0.8405 (m100) cc_final: 0.8132 (m100) REVERT: K 534 TYR cc_start: 0.8026 (m-80) cc_final: 0.7618 (m-80) REVERT: L 378 VAL cc_start: 0.1414 (OUTLIER) cc_final: 0.0937 (p) REVERT: L 553 ASP cc_start: 0.7860 (t70) cc_final: 0.7569 (t0) REVERT: L 568 MET cc_start: 0.8392 (mmp) cc_final: 0.8047 (mmm) REVERT: J 126 THR cc_start: 0.8735 (t) cc_final: 0.8366 (m) outliers start: 47 outliers final: 39 residues processed: 338 average time/residue: 0.1278 time to fit residues: 71.2720 Evaluate side-chains 328 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 387 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 520 ILE Chi-restraints excluded: chain B residue 538 VAL 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 368 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 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 567 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 416 ASP 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 99 THR 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: 9.9990 chunk 231 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.143849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100487 restraints weight = 48661.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.102657 restraints weight = 28432.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.103769 restraints weight = 18829.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104266 restraints weight = 18458.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104148 restraints weight = 15812.016| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21361 Z= 0.158 Angle : 0.624 12.173 29211 Z= 0.312 Chirality : 0.046 0.411 3415 Planarity : 0.005 0.111 3716 Dihedral : 5.156 57.877 3082 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.99 % Allowed : 20.19 % Favored : 77.82 % 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: -0.00 (0.17), residues: 2600 helix: 0.48 (0.24), residues: 467 sheet: 0.46 (0.18), residues: 820 loop : -0.40 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 491 TYR 0.033 0.002 TYR R 296 PHE 0.026 0.002 PHE G 485 TRP 0.038 0.002 TRP R 362 HIS 0.012 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00366 (21326) covalent geometry : angle 0.60676 (29129) SS BOND : bond 0.00217 ( 23) SS BOND : angle 0.77923 ( 46) hydrogen bonds : bond 0.03141 ( 666) hydrogen bonds : angle 5.17488 ( 2013) link_BETA1-4 : bond 0.01156 ( 1) link_BETA1-4 : angle 2.83729 ( 3) link_NAG-ASN : bond 0.00713 ( 11) link_NAG-ASN : angle 4.22521 ( 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 335 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 0.839 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: 0.8609 (mm-30) cc_final: 0.8262 (mm-30) REVERT: R 295 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: R 367 ASP cc_start: 0.7586 (t0) cc_final: 0.7282 (t0) REVERT: R 370 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8054 (tt0) REVERT: R 375 LYS cc_start: 0.8088 (pptt) cc_final: 0.7638 (tmmt) REVERT: B 415 GLU cc_start: 0.8068 (mp0) cc_final: 0.7748 (tm-30) REVERT: C 455 TYR cc_start: 0.7757 (m-80) cc_final: 0.7532 (m-10) REVERT: D 368 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4880 (tp) REVERT: D 562 TYR cc_start: 0.8558 (m-80) cc_final: 0.8287 (m-80) REVERT: E 364 LYS cc_start: 0.8123 (mttt) cc_final: 0.7590 (mtpp) REVERT: E 553 ASP cc_start: 0.8298 (p0) cc_final: 0.7965 (p0) REVERT: F 493 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 405 PHE cc_start: 0.5068 (OUTLIER) cc_final: 0.4341 (t80) REVERT: K 534 TYR cc_start: 0.8060 (m-80) cc_final: 0.7624 (m-80) REVERT: L 378 VAL cc_start: 0.1499 (OUTLIER) cc_final: 0.1006 (p) REVERT: L 553 ASP cc_start: 0.7641 (t70) cc_final: 0.7318 (t0) REVERT: L 568 MET cc_start: 0.8397 (mmp) cc_final: 0.8101 (mmm) REVERT: J 32 ILE cc_start: 0.8690 (mt) cc_final: 0.8391 (mm) outliers start: 47 outliers final: 41 residues processed: 321 average time/residue: 0.1274 time to fit residues: 68.0175 Evaluate side-chains 326 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 387 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 520 ILE Chi-restraints excluded: chain B residue 538 VAL 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 368 LEU Chi-restraints excluded: chain D residue 383 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 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 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 567 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 416 ASP 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 99 THR 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: 10.0000 chunk 249 optimal weight: 0.0000 chunk 155 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 246 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 HIS L 518 HIS L 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.142433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.104767 restraints weight = 48520.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105802 restraints weight = 27007.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105904 restraints weight = 19978.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106281 restraints weight = 19594.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106487 restraints weight = 17960.285| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21361 Z= 0.121 Angle : 0.613 11.870 29211 Z= 0.306 Chirality : 0.046 0.393 3415 Planarity : 0.005 0.109 3716 Dihedral : 5.083 57.048 3082 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 20.65 % 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: 0.01 (0.17), residues: 2600 helix: 0.47 (0.24), residues: 469 sheet: 0.52 (0.18), residues: 810 loop : -0.42 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 491 TYR 0.020 0.002 TYR R 296 PHE 0.025 0.001 PHE G 485 TRP 0.041 0.002 TRP R 362 HIS 0.012 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00276 (21326) covalent geometry : angle 0.59553 (29129) SS BOND : bond 0.00187 ( 23) SS BOND : angle 0.69159 ( 46) hydrogen bonds : bond 0.03052 ( 666) hydrogen bonds : angle 5.10100 ( 2013) link_BETA1-4 : bond 0.01015 ( 1) link_BETA1-4 : angle 2.90000 ( 3) link_NAG-ASN : bond 0.00703 ( 11) link_NAG-ASN : angle 4.21610 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.53 seconds wall clock time: 70 minutes 15.64 seconds (4215.64 seconds total)