Starting phenix.real_space_refine on Wed Jun 18 08:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y09_33538/06_2025/7y09_33538.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y09_33538/06_2025/7y09_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_33538/06_2025/7y09_33538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y09_33538/06_2025/7y09_33538.map" model { file = "/net/cci-nas-00/data/ceres_data/7y09_33538/06_2025/7y09_33538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y09_33538/06_2025/7y09_33538.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.23, per 1000 atoms: 0.64 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: 4.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.23 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: 7.36 Time building geometry restraints manager: 5.72 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 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.620 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 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 TRP 0.031 0.002 TRP R 362 HIS 0.013 0.001 HIS L 518 PHE 0.025 0.002 PHE C 405 TYR 0.033 0.002 TYR R 376 ARG 0.017 0.001 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.01214 ( 11) link_NAG-ASN : angle 5.34192 ( 33) link_BETA1-4 : bond 0.00961 ( 1) link_BETA1-4 : angle 1.25793 ( 3) hydrogen bonds : bond 0.25599 ( 666) hydrogen bonds : angle 9.86242 ( 2013) SS BOND : bond 0.00164 ( 23) SS BOND : angle 1.29201 ( 46) covalent geometry : bond 0.00306 (21326) covalent geometry : angle 0.67226 (29129) *********************** 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 : 2.547 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: 0.2995 time to fit residues: 206.8001 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 : 2.584 ------------------------------------------------------------------------------- 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 218 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN R 365 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.139173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097554 restraints weight = 49083.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.100128 restraints weight = 27297.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100253 restraints weight = 18343.102| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21361 Z= 0.229 Angle : 0.683 11.977 29211 Z= 0.351 Chirality : 0.049 0.565 3415 Planarity : 0.005 0.059 3716 Dihedral : 7.332 87.285 3084 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.27 % Allowed : 10.96 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2600 helix: -0.08 (0.24), residues: 461 sheet: 0.56 (0.18), residues: 835 loop : -0.53 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 354 HIS 0.009 0.002 HIS C 400 PHE 0.023 0.003 PHE R 369 TYR 0.020 0.002 TYR L 562 ARG 0.007 0.001 ARG J 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00933 ( 11) link_NAG-ASN : angle 4.68212 ( 33) link_BETA1-4 : bond 0.00482 ( 1) link_BETA1-4 : angle 1.99142 ( 3) hydrogen bonds : bond 0.04363 ( 666) hydrogen bonds : angle 6.65709 ( 2013) SS BOND : bond 0.00253 ( 23) SS BOND : angle 1.30785 ( 46) covalent geometry : bond 0.00528 (21326) covalent geometry : angle 0.66294 (29129) *********************** 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 344 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 2.343 Fit side-chains revert: symmetry clash REVERT: R 278 HIS cc_start: 0.8629 (t-90) cc_final: 0.8184 (t70) REVERT: R 295 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7301 (tm130) REVERT: R 367 ASP cc_start: 0.7967 (t0) cc_final: 0.7516 (t0) REVERT: C 455 TYR cc_start: 0.7311 (m-80) cc_final: 0.7028 (m-10) REVERT: C 534 TYR cc_start: 0.8684 (m-80) cc_final: 0.8476 (m-10) REVERT: D 391 LYS cc_start: 0.8176 (tptp) cc_final: 0.7725 (tptp) REVERT: E 364 LYS cc_start: 0.7776 (mttt) cc_final: 0.7375 (mtpp) REVERT: E 483 ASP cc_start: 0.7136 (t70) cc_final: 0.6783 (t70) REVERT: E 553 ASP cc_start: 0.8299 (p0) cc_final: 0.8035 (p0) REVERT: G 506 MET cc_start: 0.7785 (mpp) cc_final: 0.7442 (mpp) REVERT: H 453 ASP cc_start: 0.7519 (p0) cc_final: 0.7291 (p0) REVERT: K 493 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7857 (mm-40) outliers start: 30 outliers final: 18 residues processed: 331 average time/residue: 0.2955 time to fit residues: 156.4266 Evaluate side-chains 294 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 275 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain 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 F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain 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 155 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 253 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN B 402 ASN C 490 GLN D 393 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 385 GLN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN L 463 GLN ** 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 = 0.4246 r_free = 0.4246 target = 0.140550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098326 restraints weight = 48508.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101926 restraints weight = 27169.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.103632 restraints weight = 17606.255| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21361 Z= 0.124 Angle : 0.604 10.590 29211 Z= 0.304 Chirality : 0.047 0.498 3415 Planarity : 0.004 0.057 3716 Dihedral : 6.787 75.699 3082 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.57 % Allowed : 12.65 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2600 helix: 0.07 (0.23), residues: 470 sheet: 0.60 (0.18), residues: 823 loop : -0.52 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 528 HIS 0.009 0.001 HIS F 518 PHE 0.023 0.002 PHE R 117 TYR 0.019 0.001 TYR J 134 ARG 0.010 0.000 ARG H 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00981 ( 11) link_NAG-ASN : angle 4.59987 ( 33) link_BETA1-4 : bond 0.01145 ( 1) link_BETA1-4 : angle 2.74103 ( 3) hydrogen bonds : bond 0.03850 ( 666) hydrogen bonds : angle 5.94743 ( 2013) SS BOND : bond 0.00223 ( 23) SS BOND : angle 0.96103 ( 46) covalent geometry : bond 0.00278 (21326) covalent geometry : angle 0.58265 (29129) *********************** 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 357 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8168 (mm-30) REVERT: R 278 HIS cc_start: 0.8620 (t-90) cc_final: 0.8125 (t-90) REVERT: R 295 GLN cc_start: 0.7424 (tm-30) cc_final: 0.6858 (tm-30) REVERT: R 367 ASP cc_start: 0.7935 (t0) cc_final: 0.7476 (t0) REVERT: A 545 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8467 (t0) REVERT: C 455 TYR cc_start: 0.7506 (m-80) cc_final: 0.7261 (m-10) REVERT: C 534 TYR cc_start: 0.8652 (m-80) cc_final: 0.8434 (m-10) REVERT: D 499 LYS cc_start: 0.8855 (tppt) cc_final: 0.8634 (tptt) REVERT: E 364 LYS cc_start: 0.7878 (mttt) cc_final: 0.7366 (mtpp) REVERT: E 483 ASP cc_start: 0.7036 (t0) cc_final: 0.6346 (t70) REVERT: E 500 TYR cc_start: 0.8441 (p90) cc_final: 0.8034 (p90) REVERT: E 553 ASP cc_start: 0.8199 (p0) cc_final: 0.7906 (p0) REVERT: F 391 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7676 (tmtt) REVERT: G 419 ASN cc_start: 0.9028 (m-40) cc_final: 0.8812 (m110) REVERT: H 453 ASP cc_start: 0.7477 (p0) cc_final: 0.7277 (p0) REVERT: K 493 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7737 (mm-40) REVERT: K 534 TYR cc_start: 0.7957 (m-80) cc_final: 0.7694 (m-80) REVERT: J 46 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7734 (mtm-85) outliers start: 37 outliers final: 15 residues processed: 343 average time/residue: 0.2956 time to fit residues: 162.3475 Evaluate side-chains 301 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 555 SER 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 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 537 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 101 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 ASN R 199 HIS R 231 GLN R 263 ASN R 295 GLN A 545 ASN B 385 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 439 GLN L 463 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088842 restraints weight = 49282.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091913 restraints weight = 29442.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092027 restraints weight = 19134.751| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 21361 Z= 0.373 Angle : 0.788 13.736 29211 Z= 0.405 Chirality : 0.052 0.497 3415 Planarity : 0.006 0.057 3716 Dihedral : 7.027 69.446 3082 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 2.79 % Allowed : 15.95 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2600 helix: -0.21 (0.23), residues: 471 sheet: 0.20 (0.18), residues: 821 loop : -0.80 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 268 HIS 0.016 0.002 HIS E 518 PHE 0.022 0.003 PHE D 358 TYR 0.030 0.003 TYR L 562 ARG 0.011 0.001 ARG D 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01009 ( 11) link_NAG-ASN : angle 4.96653 ( 33) link_BETA1-4 : bond 0.00835 ( 1) link_BETA1-4 : angle 2.54067 ( 3) hydrogen bonds : bond 0.04191 ( 666) hydrogen bonds : angle 6.33029 ( 2013) SS BOND : bond 0.00421 ( 23) SS BOND : angle 1.36103 ( 46) covalent geometry : bond 0.00861 (21326) covalent geometry : angle 0.76877 (29129) *********************** 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 358 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 292 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 172 TRP cc_start: 0.9048 (p-90) cc_final: 0.8847 (p-90) REVERT: R 278 HIS cc_start: 0.8694 (t-90) cc_final: 0.8147 (t-90) REVERT: R 295 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7330 (tm130) REVERT: R 367 ASP cc_start: 0.7961 (t0) cc_final: 0.7481 (t0) REVERT: R 370 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8242 (tt0) REVERT: A 455 TYR cc_start: 0.8740 (m-80) cc_final: 0.8510 (m-10) REVERT: A 545 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8468 (t0) REVERT: B 354 PHE cc_start: 0.8582 (t80) cc_final: 0.8361 (t80) REVERT: B 415 GLU cc_start: 0.8208 (mp0) cc_final: 0.7998 (mp0) REVERT: C 455 TYR cc_start: 0.7904 (m-80) cc_final: 0.7655 (m-10) REVERT: C 465 ASN cc_start: 0.8937 (t0) cc_final: 0.8572 (t0) REVERT: C 510 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8065 (mm-40) REVERT: D 368 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.5057 (tp) REVERT: D 391 LYS cc_start: 0.8356 (tptp) cc_final: 0.7772 (tptp) REVERT: E 364 LYS cc_start: 0.7990 (mttt) cc_final: 0.7451 (mtpp) REVERT: E 483 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6696 (t70) REVERT: E 553 ASP cc_start: 0.8506 (p0) cc_final: 0.8183 (p0) REVERT: E 555 SER cc_start: 0.8067 (m) cc_final: 0.7864 (m) REVERT: F 493 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7863 (tm-30) REVERT: G 419 ASN cc_start: 0.9022 (m-40) cc_final: 0.8816 (m110) REVERT: H 453 ASP cc_start: 0.7786 (p0) cc_final: 0.7364 (p0) REVERT: H 463 GLN cc_start: 0.8556 (tt0) cc_final: 0.8220 (tt0) REVERT: K 493 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7913 (mm-40) REVERT: K 500 TYR cc_start: 0.8763 (p90) cc_final: 0.8470 (p90) REVERT: L 545 ASN cc_start: 0.8011 (t160) cc_final: 0.7779 (t0) REVERT: J 46 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7929 (mtt-85) outliers start: 66 outliers final: 40 residues processed: 341 average time/residue: 0.2934 time to fit residues: 160.6978 Evaluate side-chains 302 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 A residue 541 GLU Chi-restraints excluded: chain A residue 545 ASN 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 385 GLN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 417 ASP 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 417 ASP Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 164 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 88 optimal weight: 0.0170 chunk 196 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN A 510 GLN A 545 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.136625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092490 restraints weight = 48951.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.095525 restraints weight = 26692.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097388 restraints weight = 19024.727| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3377 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= 0.131 Angle : 0.624 12.488 29211 Z= 0.314 Chirality : 0.047 0.448 3415 Planarity : 0.004 0.058 3716 Dihedral : 6.343 63.209 3082 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.58 % Allowed : 17.60 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2600 helix: 0.07 (0.23), residues: 471 sheet: 0.27 (0.18), residues: 821 loop : -0.56 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 488 HIS 0.009 0.001 HIS L 518 PHE 0.017 0.002 PHE R 117 TYR 0.019 0.002 TYR L 562 ARG 0.010 0.000 ARG D 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 11) link_NAG-ASN : angle 4.75708 ( 33) link_BETA1-4 : bond 0.01169 ( 1) link_BETA1-4 : angle 2.73600 ( 3) hydrogen bonds : bond 0.03451 ( 666) hydrogen bonds : angle 5.65904 ( 2013) SS BOND : bond 0.00200 ( 23) SS BOND : angle 0.93724 ( 46) covalent geometry : bond 0.00296 (21326) covalent geometry : angle 0.60238 (29129) *********************** 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 372 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 2.558 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 272 MET cc_start: 0.7512 (mmm) cc_final: 0.7081 (mmm) REVERT: R 290 MET cc_start: 0.7896 (pmm) cc_final: 0.6566 (ptt) REVERT: R 291 ASP cc_start: 0.7161 (m-30) cc_final: 0.6831 (m-30) REVERT: R 293 ILE cc_start: 0.8806 (pt) cc_final: 0.8600 (pt) REVERT: R 295 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7077 (tm130) REVERT: R 367 ASP cc_start: 0.7735 (t0) cc_final: 0.7266 (t0) REVERT: R 370 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8131 (tt0) REVERT: R 375 LYS cc_start: 0.7901 (pptt) cc_final: 0.7646 (tmmt) REVERT: A 574 THR cc_start: 0.5631 (m) cc_final: 0.5380 (p) REVERT: B 463 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8310 (mm-40) REVERT: C 455 TYR cc_start: 0.7732 (m-80) cc_final: 0.7465 (m-10) REVERT: D 368 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4575 (tp) REVERT: D 562 TYR cc_start: 0.8518 (m-80) cc_final: 0.8267 (m-80) REVERT: E 364 LYS cc_start: 0.8098 (mttt) cc_final: 0.7531 (mtpp) REVERT: E 483 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6390 (t70) REVERT: E 553 ASP cc_start: 0.8433 (p0) cc_final: 0.8135 (p0) REVERT: F 391 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7476 (tmtt) REVERT: F 493 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7905 (tm-30) REVERT: G 405 PHE cc_start: 0.5488 (OUTLIER) cc_final: 0.4401 (t80) REVERT: G 419 ASN cc_start: 0.9039 (m-40) cc_final: 0.8786 (m110) REVERT: H 453 ASP cc_start: 0.7641 (p0) cc_final: 0.7311 (p0) REVERT: K 500 TYR cc_start: 0.8647 (p90) cc_final: 0.8421 (p90) REVERT: K 534 TYR cc_start: 0.8296 (m-80) cc_final: 0.7753 (m-80) REVERT: L 455 TYR cc_start: 0.5651 (m-80) cc_final: 0.5083 (m-80) REVERT: J 46 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7661 (mtt-85) outliers start: 61 outliers final: 33 residues processed: 357 average time/residue: 0.2828 time to fit residues: 165.7085 Evaluate side-chains 318 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 541 GLU 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 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 416 ASP 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 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 535 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 51 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 48 optimal weight: 0.0570 chunk 188 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 241 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 ASN A 510 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.136940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093376 restraints weight = 48596.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097113 restraints weight = 27778.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098145 restraints weight = 17991.753| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21361 Z= 0.131 Angle : 0.616 12.425 29211 Z= 0.307 Chirality : 0.047 0.409 3415 Planarity : 0.004 0.058 3716 Dihedral : 5.951 56.095 3082 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.24 % Allowed : 19.13 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2600 helix: 0.14 (0.23), residues: 477 sheet: 0.24 (0.18), residues: 808 loop : -0.52 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 172 HIS 0.011 0.001 HIS L 518 PHE 0.016 0.002 PHE F 354 TYR 0.022 0.002 TYR J 101 ARG 0.009 0.000 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 11) link_NAG-ASN : angle 4.55428 ( 33) link_BETA1-4 : bond 0.01246 ( 1) link_BETA1-4 : angle 2.92201 ( 3) hydrogen bonds : bond 0.03295 ( 666) hydrogen bonds : angle 5.43847 ( 2013) SS BOND : bond 0.00262 ( 23) SS BOND : angle 1.07713 ( 46) covalent geometry : bond 0.00304 (21326) covalent geometry : angle 0.59504 (29129) *********************** 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 358 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 2.451 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 269 ASP cc_start: 0.8791 (m-30) cc_final: 0.8386 (p0) REVERT: R 272 MET cc_start: 0.7567 (mmm) cc_final: 0.7198 (mmm) REVERT: R 290 MET cc_start: 0.7774 (pmm) cc_final: 0.6782 (ptt) REVERT: R 367 ASP cc_start: 0.7827 (t0) cc_final: 0.7428 (t0) REVERT: R 370 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8179 (tt0) REVERT: R 375 LYS cc_start: 0.8109 (pptt) cc_final: 0.7815 (tmmt) REVERT: B 415 GLU cc_start: 0.8076 (mp0) cc_final: 0.7834 (mp0) REVERT: B 463 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8343 (mm-40) REVERT: C 455 TYR cc_start: 0.7748 (m-80) cc_final: 0.7525 (m-10) REVERT: D 368 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4823 (tp) REVERT: D 562 TYR cc_start: 0.8531 (m-80) cc_final: 0.8304 (m-80) REVERT: E 364 LYS cc_start: 0.8049 (mttt) cc_final: 0.7479 (mtpp) REVERT: E 553 ASP cc_start: 0.8434 (p0) cc_final: 0.8115 (p0) REVERT: F 391 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7547 (tmtt) REVERT: F 493 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 405 PHE cc_start: 0.5363 (OUTLIER) cc_final: 0.4452 (t80) REVERT: G 419 ASN cc_start: 0.9052 (m-40) cc_final: 0.8790 (m110) REVERT: H 453 ASP cc_start: 0.7557 (p0) cc_final: 0.7261 (p0) REVERT: K 534 TYR cc_start: 0.8144 (m-80) cc_final: 0.7615 (m-80) REVERT: L 455 TYR cc_start: 0.5777 (m-80) cc_final: 0.5239 (m-80) REVERT: J 46 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7706 (mtt-85) outliers start: 53 outliers final: 36 residues processed: 343 average time/residue: 0.2702 time to fit residues: 151.2366 Evaluate side-chains 323 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 541 GLU 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 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 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 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 535 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 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 175 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 142 optimal weight: 30.0000 chunk 177 optimal weight: 0.0010 chunk 117 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN A 393 HIS A 510 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN K 450 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.136614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093050 restraints weight = 48656.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096713 restraints weight = 28024.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097665 restraints weight = 18095.123| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3535 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= 0.144 Angle : 0.616 12.322 29211 Z= 0.308 Chirality : 0.046 0.398 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.665 56.771 3082 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.41 % Allowed : 20.19 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2600 helix: 0.27 (0.23), residues: 471 sheet: 0.34 (0.18), residues: 808 loop : -0.48 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 PHE 0.022 0.002 PHE L 424 TYR 0.019 0.002 TYR K 500 ARG 0.008 0.000 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 11) link_NAG-ASN : angle 4.44614 ( 33) link_BETA1-4 : bond 0.01219 ( 1) link_BETA1-4 : angle 2.97259 ( 3) hydrogen bonds : bond 0.03205 ( 666) hydrogen bonds : angle 5.33248 ( 2013) SS BOND : bond 0.00219 ( 23) SS BOND : angle 0.94573 ( 46) covalent geometry : bond 0.00336 (21326) covalent geometry : angle 0.59635 (29129) *********************** 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 355 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 2.496 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 290 MET cc_start: 0.7660 (pmm) cc_final: 0.7322 (ptt) REVERT: R 295 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7053 (tm130) REVERT: R 367 ASP cc_start: 0.7781 (t0) cc_final: 0.7407 (t0) REVERT: R 370 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8163 (tt0) REVERT: R 375 LYS cc_start: 0.8153 (pptt) cc_final: 0.7825 (tmmt) REVERT: A 455 TYR cc_start: 0.8757 (m-80) cc_final: 0.8236 (m-80) REVERT: B 415 GLU cc_start: 0.8098 (mp0) cc_final: 0.7896 (mp0) REVERT: B 463 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8358 (mm-40) REVERT: C 455 TYR cc_start: 0.7771 (m-80) cc_final: 0.7570 (m-10) REVERT: D 368 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4799 (tp) REVERT: E 364 LYS cc_start: 0.8086 (mttt) cc_final: 0.7493 (mtpp) REVERT: E 553 ASP cc_start: 0.8407 (p0) cc_final: 0.8092 (p0) REVERT: F 391 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7592 (tmtt) REVERT: F 493 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7943 (tm-30) REVERT: G 405 PHE cc_start: 0.5178 (t80) cc_final: 0.4302 (t80) REVERT: G 419 ASN cc_start: 0.9052 (m-40) cc_final: 0.8792 (m110) REVERT: H 453 ASP cc_start: 0.7589 (p0) cc_final: 0.7206 (p0) REVERT: K 534 TYR cc_start: 0.8141 (m-80) cc_final: 0.7606 (m-80) REVERT: L 553 ASP cc_start: 0.7830 (t70) cc_final: 0.7558 (t0) REVERT: L 568 MET cc_start: 0.8430 (mmp) cc_final: 0.8193 (mmm) REVERT: J 46 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7648 (mtt-85) outliers start: 57 outliers final: 41 residues processed: 341 average time/residue: 0.2821 time to fit residues: 155.8726 Evaluate side-chains 325 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 2.325 ------------------------------------------------------------------------------- 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 392 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 562 TYR 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 564 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 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 F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 126 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN C 545 ASN H 463 GLN ** K 430 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094593 restraints weight = 49015.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095623 restraints weight = 28848.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095928 restraints weight = 21474.408| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21361 Z= 0.172 Angle : 0.627 12.303 29211 Z= 0.314 Chirality : 0.047 0.396 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.533 56.238 3082 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.29 % Allowed : 20.65 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2600 helix: 0.28 (0.23), residues: 464 sheet: 0.25 (0.18), residues: 812 loop : -0.46 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 PHE 0.034 0.002 PHE G 485 TYR 0.019 0.002 TYR L 562 ARG 0.012 0.000 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 11) link_NAG-ASN : angle 4.40911 ( 33) link_BETA1-4 : bond 0.00994 ( 1) link_BETA1-4 : angle 2.93775 ( 3) hydrogen bonds : bond 0.03321 ( 666) hydrogen bonds : angle 5.35747 ( 2013) SS BOND : bond 0.00233 ( 23) SS BOND : angle 0.91790 ( 46) covalent geometry : bond 0.00400 (21326) covalent geometry : angle 0.60818 (29129) *********************** 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 335 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 295 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7355 (tm130) REVERT: R 367 ASP cc_start: 0.7645 (t0) cc_final: 0.7338 (t0) REVERT: R 370 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8177 (tt0) REVERT: R 375 LYS cc_start: 0.8122 (pptt) cc_final: 0.7735 (tmmt) REVERT: A 455 TYR cc_start: 0.8771 (m-80) cc_final: 0.8294 (m-80) REVERT: B 416 ASP cc_start: 0.8648 (p0) cc_final: 0.8347 (t0) REVERT: C 455 TYR cc_start: 0.7833 (m-80) cc_final: 0.7616 (m-10) REVERT: D 368 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4781 (tp) REVERT: E 364 LYS cc_start: 0.8155 (mttt) cc_final: 0.7537 (mtpp) REVERT: E 553 ASP cc_start: 0.8488 (p0) cc_final: 0.8165 (p0) REVERT: G 405 PHE cc_start: 0.5149 (t80) cc_final: 0.4252 (t80) REVERT: G 419 ASN cc_start: 0.9046 (m-40) cc_final: 0.8791 (m110) REVERT: H 453 ASP cc_start: 0.7713 (p0) cc_final: 0.7319 (p0) REVERT: K 500 TYR cc_start: 0.8672 (p90) cc_final: 0.8369 (p90) REVERT: K 534 TYR cc_start: 0.8262 (m-80) cc_final: 0.7682 (m-80) REVERT: L 378 VAL cc_start: 0.1666 (OUTLIER) cc_final: 0.1203 (p) REVERT: L 490 GLN cc_start: 0.5701 (pt0) cc_final: 0.5347 (pt0) REVERT: L 553 ASP cc_start: 0.7865 (t70) cc_final: 0.7536 (t0) REVERT: L 568 MET cc_start: 0.8518 (mmp) cc_final: 0.8307 (mmm) REVERT: J 46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7659 (mtt-85) outliers start: 54 outliers final: 46 residues processed: 324 average time/residue: 0.2867 time to fit residues: 152.4406 Evaluate side-chains 322 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 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 392 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 562 TYR 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 564 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 C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 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 198 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 213 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN A 510 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS L 545 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.136452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.092518 restraints weight = 48716.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095530 restraints weight = 26339.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.097396 restraints weight = 18694.461| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3720 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= 0.142 Angle : 0.622 11.947 29211 Z= 0.310 Chirality : 0.046 0.384 3415 Planarity : 0.004 0.058 3716 Dihedral : 5.416 57.881 3082 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.37 % Allowed : 20.91 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2600 helix: 0.29 (0.23), residues: 467 sheet: 0.27 (0.18), residues: 805 loop : -0.46 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 PHE 0.029 0.002 PHE G 485 TYR 0.018 0.002 TYR L 562 ARG 0.013 0.000 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 11) link_NAG-ASN : angle 4.36444 ( 33) link_BETA1-4 : bond 0.01140 ( 1) link_BETA1-4 : angle 2.94016 ( 3) hydrogen bonds : bond 0.03201 ( 666) hydrogen bonds : angle 5.26278 ( 2013) SS BOND : bond 0.00203 ( 23) SS BOND : angle 0.84947 ( 46) covalent geometry : bond 0.00331 (21326) covalent geometry : angle 0.60352 (29129) *********************** 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 341 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 2.519 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 295 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7067 (tm130) REVERT: R 361 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8451 (mt-10) REVERT: R 367 ASP cc_start: 0.7497 (t0) cc_final: 0.7218 (t0) REVERT: R 370 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8107 (tt0) REVERT: R 375 LYS cc_start: 0.7972 (pptt) cc_final: 0.7594 (tmmt) REVERT: A 455 TYR cc_start: 0.8741 (m-80) cc_final: 0.8286 (m-80) REVERT: B 415 GLU cc_start: 0.7847 (mp0) cc_final: 0.7588 (tm-30) REVERT: B 416 ASP cc_start: 0.8499 (p0) cc_final: 0.7527 (t0) REVERT: D 368 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4631 (tp) REVERT: E 364 LYS cc_start: 0.8223 (mttt) cc_final: 0.7592 (mtpp) REVERT: E 553 ASP cc_start: 0.8409 (p0) cc_final: 0.7999 (p0) REVERT: F 391 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7561 (tmtt) REVERT: F 493 GLN cc_start: 0.8296 (tm-30) cc_final: 0.8024 (tm-30) REVERT: G 405 PHE cc_start: 0.5199 (OUTLIER) cc_final: 0.4327 (t80) REVERT: G 419 ASN cc_start: 0.9028 (m-40) cc_final: 0.8765 (m110) REVERT: H 453 ASP cc_start: 0.7633 (p0) cc_final: 0.7242 (p0) REVERT: K 500 TYR cc_start: 0.8644 (p90) cc_final: 0.8362 (p90) REVERT: K 534 TYR cc_start: 0.8206 (m-80) cc_final: 0.7654 (m-80) REVERT: L 378 VAL cc_start: 0.1755 (OUTLIER) cc_final: 0.1288 (p) REVERT: L 568 MET cc_start: 0.8499 (mmp) cc_final: 0.8298 (mmm) outliers start: 56 outliers final: 42 residues processed: 328 average time/residue: 0.3203 time to fit residues: 173.0655 Evaluate side-chains 319 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 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 392 THR Chi-restraints excluded: chain A residue 541 GLU 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 564 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain 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 G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 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 130 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 209 optimal weight: 0.0070 chunk 171 optimal weight: 0.0030 chunk 89 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.4208 ------------------------------------------------------------------------------- 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 ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4289 r_free = 0.4289 target = 0.141756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.104068 restraints weight = 48360.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105132 restraints weight = 26985.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105083 restraints weight = 19972.939| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21361 Z= 0.115 Angle : 0.621 11.710 29211 Z= 0.309 Chirality : 0.046 0.388 3415 Planarity : 0.005 0.119 3716 Dihedral : 5.250 58.950 3082 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.95 % Allowed : 21.24 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2600 helix: 0.35 (0.24), residues: 466 sheet: 0.33 (0.18), residues: 813 loop : -0.43 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 362 HIS 0.012 0.001 HIS F 518 PHE 0.029 0.001 PHE G 485 TYR 0.020 0.002 TYR C 455 ARG 0.014 0.000 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 11) link_NAG-ASN : angle 4.28357 ( 33) link_BETA1-4 : bond 0.00823 ( 1) link_BETA1-4 : angle 2.96385 ( 3) hydrogen bonds : bond 0.03169 ( 666) hydrogen bonds : angle 5.13101 ( 2013) SS BOND : bond 0.00176 ( 23) SS BOND : angle 0.74886 ( 46) covalent geometry : bond 0.00261 (21326) covalent geometry : angle 0.60346 (29129) ********************** 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 349 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 303 time to evaluate : 2.603 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 295 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7174 (tm130) REVERT: R 367 ASP cc_start: 0.7575 (t0) cc_final: 0.7292 (t0) REVERT: R 370 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8104 (tt0) REVERT: R 375 LYS cc_start: 0.8057 (pptt) cc_final: 0.7639 (tmmt) REVERT: A 445 LYS cc_start: 0.8386 (tppt) cc_final: 0.7307 (tttm) REVERT: A 455 TYR cc_start: 0.8789 (m-80) cc_final: 0.8399 (m-80) REVERT: B 416 ASP cc_start: 0.8574 (p0) cc_final: 0.8284 (t0) REVERT: E 364 LYS cc_start: 0.8195 (mttt) cc_final: 0.7558 (mtpp) REVERT: E 553 ASP cc_start: 0.8333 (p0) cc_final: 0.8016 (p0) REVERT: F 391 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7571 (tmtt) REVERT: G 405 PHE cc_start: 0.4991 (t80) cc_final: 0.4292 (t80) REVERT: G 419 ASN cc_start: 0.9042 (m-40) cc_final: 0.8782 (m110) REVERT: H 453 ASP cc_start: 0.7647 (p0) cc_final: 0.7351 (p0) REVERT: K 534 TYR cc_start: 0.8080 (m-80) cc_final: 0.7622 (m-80) REVERT: L 378 VAL cc_start: 0.1604 (OUTLIER) cc_final: 0.1122 (p) REVERT: L 568 MET cc_start: 0.8324 (mmp) cc_final: 0.8116 (mmm) outliers start: 46 outliers final: 32 residues processed: 338 average time/residue: 0.2955 time to fit residues: 163.5665 Evaluate side-chains 315 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain R residue 315 PHE 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 538 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 363 THR 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 483 ASP Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 416 ASP Chi-restraints excluded: chain L residue 516 PHE 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 206 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 chunk 257 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 210 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.140010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.100558 restraints weight = 48735.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102109 restraints weight = 28674.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101888 restraints weight = 20405.119| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21361 Z= 0.173 Angle : 0.648 11.973 29211 Z= 0.326 Chirality : 0.047 0.399 3415 Planarity : 0.005 0.108 3716 Dihedral : 5.276 58.310 3082 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.90 % Allowed : 21.71 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2600 helix: 0.35 (0.24), residues: 466 sheet: 0.29 (0.18), residues: 805 loop : -0.45 (0.18), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 488 HIS 0.011 0.001 HIS L 518 PHE 0.025 0.002 PHE G 485 TYR 0.019 0.002 TYR K 500 ARG 0.014 0.000 ARG F 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 11) link_NAG-ASN : angle 4.29097 ( 33) link_BETA1-4 : bond 0.00960 ( 1) link_BETA1-4 : angle 2.79696 ( 3) hydrogen bonds : bond 0.03224 ( 666) hydrogen bonds : angle 5.28810 ( 2013) SS BOND : bond 0.00233 ( 23) SS BOND : angle 0.84744 ( 46) covalent geometry : bond 0.00405 (21326) covalent geometry : angle 0.63095 (29129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7263.02 seconds wall clock time: 126 minutes 48.94 seconds (7608.94 seconds total)