Starting phenix.real_space_refine on Wed Nov 20 05:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y09_33538/11_2024/7y09_33538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y09_33538/11_2024/7y09_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y09_33538/11_2024/7y09_33538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y09_33538/11_2024/7y09_33538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y09_33538/11_2024/7y09_33538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y09_33538/11_2024/7y09_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 13.70, per 1000 atoms: 0.66 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: 4.68 Conformation dependent library (CDL) restraints added in 2.6 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: 3.13 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: 7.99 Time building geometry restraints manager: 5.38 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 48.440 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- 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 21326 Z= 0.207 Angle : 0.672 10.765 29129 Z= 0.357 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 *********************** 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 : 2.443 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: 0.3288 time to fit residues: 228.1009 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 : 2.523 ------------------------------------------------------------------------------- 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: 5.9990 chunk 235 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN R 295 GLN R 365 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21326 Z= 0.423 Angle : 0.710 13.009 29129 Z= 0.370 Chirality : 0.051 0.602 3415 Planarity : 0.005 0.059 3716 Dihedral : 7.446 87.908 3084 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.52 % Allowed : 11.13 % Favored : 87.35 % 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: -0.27 (0.16), residues: 2600 helix: -0.13 (0.24), residues: 462 sheet: 0.51 (0.18), residues: 820 loop : -0.58 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 354 HIS 0.010 0.002 HIS E 518 PHE 0.026 0.003 PHE E 354 TYR 0.023 0.002 TYR L 562 ARG 0.008 0.001 ARG J 57 *********************** 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 353 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 2.288 Fit side-chains revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8369 (mm-30) REVERT: R 278 HIS cc_start: 0.8603 (t-90) cc_final: 0.8183 (t70) REVERT: R 295 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7408 (tm130) REVERT: R 367 ASP cc_start: 0.7939 (t0) cc_final: 0.7521 (t0) REVERT: R 370 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8090 (tt0) REVERT: A 564 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7977 (p) REVERT: C 455 TYR cc_start: 0.7397 (m-80) cc_final: 0.7048 (m-10) REVERT: D 391 LYS cc_start: 0.8124 (tptp) cc_final: 0.7705 (tptp) REVERT: E 364 LYS cc_start: 0.7879 (mttt) cc_final: 0.7453 (mtpp) REVERT: E 483 ASP cc_start: 0.7034 (t0) cc_final: 0.6697 (t70) REVERT: E 553 ASP cc_start: 0.8260 (p0) cc_final: 0.7949 (p0) REVERT: G 506 MET cc_start: 0.7875 (mpp) cc_final: 0.7579 (mpp) REVERT: H 453 ASP cc_start: 0.7571 (p0) cc_final: 0.7188 (p0) REVERT: K 493 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7724 (mm-40) outliers start: 36 outliers final: 20 residues processed: 338 average time/residue: 0.3196 time to fit residues: 172.5928 Evaluate side-chains 287 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 295 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 515 TYR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain 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 130 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 233 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN B 385 GLN B 463 GLN C 487 GLN C 490 GLN D 393 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21326 Z= 0.186 Angle : 0.591 10.024 29129 Z= 0.303 Chirality : 0.047 0.498 3415 Planarity : 0.004 0.055 3716 Dihedral : 6.878 76.454 3082 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.82 % Allowed : 13.50 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2600 helix: 0.01 (0.23), residues: 471 sheet: 0.52 (0.18), residues: 819 loop : -0.53 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 268 HIS 0.009 0.001 HIS E 518 PHE 0.021 0.002 PHE R 117 TYR 0.019 0.002 TYR J 134 ARG 0.011 0.000 ARG H 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5200 Ramachandran restraints generated. 2600 Oldfield, 0 Emsley, 2600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 315 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8323 (mm-30) REVERT: R 278 HIS cc_start: 0.8601 (t-90) cc_final: 0.8107 (t-90) REVERT: R 295 GLN cc_start: 0.7486 (tm-30) cc_final: 0.6889 (tm-30) REVERT: R 367 ASP cc_start: 0.7868 (t0) cc_final: 0.7438 (t0) REVERT: R 370 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8033 (tt0) REVERT: A 545 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8394 (t0) REVERT: C 455 TYR cc_start: 0.7411 (m-80) cc_final: 0.7109 (m-10) REVERT: C 534 TYR cc_start: 0.8618 (m-80) cc_final: 0.8388 (m-10) REVERT: D 499 LYS cc_start: 0.8839 (tppt) cc_final: 0.8621 (tptt) REVERT: E 364 LYS cc_start: 0.7949 (mttt) cc_final: 0.7423 (mtpp) REVERT: E 483 ASP cc_start: 0.6964 (t0) cc_final: 0.6301 (t70) REVERT: E 553 ASP cc_start: 0.8158 (p0) cc_final: 0.7860 (p0) REVERT: F 391 LYS cc_start: 0.7709 (ptpt) cc_final: 0.7315 (tmtt) REVERT: G 419 ASN cc_start: 0.8995 (m-40) cc_final: 0.8768 (m110) REVERT: H 453 ASP cc_start: 0.7617 (p0) cc_final: 0.7288 (p0) REVERT: H 547 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8869 (t) REVERT: K 493 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7700 (mm-40) REVERT: K 534 TYR cc_start: 0.7987 (m-80) cc_final: 0.7665 (m-80) REVERT: J 46 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7653 (mtm-85) outliers start: 43 outliers final: 20 residues processed: 344 average time/residue: 0.3094 time to fit residues: 170.4181 Evaluate side-chains 299 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 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 99 THR 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 232 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 295 GLN A 545 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 439 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21326 Z= 0.481 Angle : 0.713 12.384 29129 Z= 0.371 Chirality : 0.050 0.489 3415 Planarity : 0.005 0.057 3716 Dihedral : 6.877 69.396 3082 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.75 % Allowed : 15.95 % Favored : 81.29 % 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: -0.47 (0.16), residues: 2600 helix: -0.09 (0.23), residues: 472 sheet: 0.23 (0.18), residues: 816 loop : -0.67 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 488 HIS 0.014 0.002 HIS E 518 PHE 0.023 0.003 PHE D 358 TYR 0.027 0.002 TYR L 562 ARG 0.012 0.001 ARG G 491 *********************** 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 355 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8444 (mm-30) REVERT: R 278 HIS cc_start: 0.8674 (t-90) cc_final: 0.8133 (t-90) REVERT: R 290 MET cc_start: 0.8079 (pmm) cc_final: 0.6751 (ptt) REVERT: R 291 ASP cc_start: 0.7619 (m-30) cc_final: 0.6687 (m-30) REVERT: R 295 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7165 (tm130) REVERT: R 367 ASP cc_start: 0.7920 (t0) cc_final: 0.7442 (t0) REVERT: R 370 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8191 (tt0) REVERT: A 545 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8457 (t0) REVERT: C 455 TYR cc_start: 0.7696 (m-80) cc_final: 0.7385 (m-10) REVERT: C 465 ASN cc_start: 0.8985 (t0) cc_final: 0.8622 (t0) REVERT: C 510 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7980 (mm-40) REVERT: D 368 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5138 (tp) REVERT: E 364 LYS cc_start: 0.8092 (mttt) cc_final: 0.7545 (mtpp) REVERT: E 483 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6582 (t70) REVERT: E 553 ASP cc_start: 0.8461 (p0) cc_final: 0.8123 (p0) REVERT: F 493 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 419 ASN cc_start: 0.9014 (m-40) cc_final: 0.8787 (m110) REVERT: H 453 ASP cc_start: 0.7794 (p0) cc_final: 0.7270 (p0) REVERT: H 463 GLN cc_start: 0.8618 (tt0) cc_final: 0.8374 (tt0) REVERT: K 500 TYR cc_start: 0.8684 (p90) cc_final: 0.8385 (p90) REVERT: K 534 TYR cc_start: 0.8446 (m-80) cc_final: 0.7859 (m-80) REVERT: L 545 ASN cc_start: 0.7997 (t160) cc_final: 0.7763 (t0) REVERT: L 568 MET cc_start: 0.8516 (mmp) cc_final: 0.8307 (mmm) REVERT: J 46 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7733 (mtt-85) outliers start: 65 outliers final: 46 residues processed: 336 average time/residue: 0.3297 time to fit residues: 180.9022 Evaluate side-chains 316 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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 545 ASN Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 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 C residue 561 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 555 SER 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 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 3 optimal weight: 0.1980 chunk 186 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21326 Z= 0.216 Angle : 0.600 10.632 29129 Z= 0.308 Chirality : 0.047 0.442 3415 Planarity : 0.004 0.057 3716 Dihedral : 6.363 63.632 3082 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.79 % Allowed : 17.73 % Favored : 79.48 % 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: -0.31 (0.16), residues: 2600 helix: 0.09 (0.23), residues: 471 sheet: 0.25 (0.18), residues: 836 loop : -0.54 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 172 HIS 0.009 0.001 HIS L 518 PHE 0.027 0.002 PHE R 117 TYR 0.020 0.002 TYR L 562 ARG 0.008 0.000 ARG F 491 *********************** 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 365 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8365 (mm-30) REVERT: R 290 MET cc_start: 0.7695 (pmm) cc_final: 0.6887 (ptt) REVERT: R 291 ASP cc_start: 0.7167 (m-30) cc_final: 0.6625 (m-30) REVERT: R 295 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7056 (tm-30) REVERT: R 367 ASP cc_start: 0.7782 (t0) cc_final: 0.7309 (t0) REVERT: R 370 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8133 (tt0) REVERT: A 455 TYR cc_start: 0.8607 (m-80) cc_final: 0.8148 (m-80) REVERT: A 574 THR cc_start: 0.5615 (m) cc_final: 0.5355 (p) REVERT: C 455 TYR cc_start: 0.7570 (m-80) cc_final: 0.7267 (m-10) REVERT: D 368 LEU cc_start: 0.5135 (OUTLIER) cc_final: 0.4869 (tp) REVERT: E 364 LYS cc_start: 0.8121 (mttt) cc_final: 0.7545 (mtpp) REVERT: E 553 ASP cc_start: 0.8381 (p0) cc_final: 0.8078 (p0) REVERT: F 493 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7963 (tm-30) REVERT: G 405 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4315 (t80) REVERT: G 419 ASN cc_start: 0.9045 (m-40) cc_final: 0.8796 (m110) REVERT: H 453 ASP cc_start: 0.7633 (p0) cc_final: 0.7248 (p0) REVERT: K 500 TYR cc_start: 0.8590 (p90) cc_final: 0.8376 (p90) REVERT: K 534 TYR cc_start: 0.8283 (m-80) cc_final: 0.7785 (m-80) REVERT: L 455 TYR cc_start: 0.5701 (m-80) cc_final: 0.5102 (m-80) REVERT: J 46 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7621 (mtt-85) outliers start: 66 outliers final: 39 residues processed: 349 average time/residue: 0.2949 time to fit residues: 167.1004 Evaluate side-chains 315 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain 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 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 555 SER 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 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 535 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 250 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN D 385 GLN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN ** H 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.005 0.055 21326 Z= 0.322 Angle : 0.627 10.960 29129 Z= 0.320 Chirality : 0.048 0.429 3415 Planarity : 0.004 0.057 3716 Dihedral : 6.161 58.113 3082 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.84 % Allowed : 18.66 % Favored : 78.50 % 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: -0.36 (0.17), residues: 2600 helix: 0.11 (0.23), residues: 478 sheet: 0.22 (0.18), residues: 827 loop : -0.60 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 488 HIS 0.010 0.001 HIS L 518 PHE 0.015 0.002 PHE G 358 TYR 0.022 0.002 TYR L 562 ARG 0.010 0.000 ARG F 491 *********************** 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 354 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 2.447 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8410 (mm-30) REVERT: R 290 MET cc_start: 0.7818 (pmm) cc_final: 0.7378 (ptt) REVERT: R 367 ASP cc_start: 0.7821 (t0) cc_final: 0.7376 (t0) REVERT: R 370 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8191 (tt0) REVERT: A 574 THR cc_start: 0.6248 (m) cc_final: 0.6012 (p) REVERT: C 455 TYR cc_start: 0.7683 (m-80) cc_final: 0.7433 (m-10) REVERT: D 368 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.5078 (tp) REVERT: D 562 TYR cc_start: 0.8535 (m-80) cc_final: 0.8308 (m-80) REVERT: E 364 LYS cc_start: 0.8142 (mttt) cc_final: 0.7562 (mtpp) REVERT: E 483 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6281 (t70) REVERT: E 553 ASP cc_start: 0.8446 (p0) cc_final: 0.8107 (p0) REVERT: F 489 MET cc_start: 0.8664 (mmp) cc_final: 0.8372 (mmm) REVERT: F 493 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7979 (tm-30) REVERT: G 405 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.4322 (t80) REVERT: G 419 ASN cc_start: 0.9045 (m-40) cc_final: 0.8793 (m110) REVERT: H 453 ASP cc_start: 0.7694 (p0) cc_final: 0.7214 (p0) REVERT: K 500 TYR cc_start: 0.8663 (p90) cc_final: 0.8411 (p90) REVERT: K 534 TYR cc_start: 0.8358 (m-80) cc_final: 0.7804 (m-80) REVERT: L 455 TYR cc_start: 0.5813 (m-80) cc_final: 0.5187 (m-80) REVERT: J 46 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7657 (mtt-85) outliers start: 67 outliers final: 47 residues processed: 340 average time/residue: 0.2976 time to fit residues: 164.5765 Evaluate side-chains 318 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 561 LEU 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 501 VAL 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 535 THR Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 0.0000 chunk 28 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 152 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21326 Z= 0.229 Angle : 0.604 11.058 29129 Z= 0.306 Chirality : 0.046 0.406 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.842 54.965 3082 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.50 % Allowed : 19.89 % Favored : 77.61 % 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: -0.27 (0.17), residues: 2600 helix: 0.17 (0.23), residues: 479 sheet: 0.26 (0.18), residues: 825 loop : -0.53 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 362 HIS 0.010 0.001 HIS L 518 PHE 0.029 0.002 PHE R 117 TYR 0.022 0.002 TYR E 455 ARG 0.009 0.000 ARG F 491 *********************** 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 358 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8382 (mm-30) REVERT: R 290 MET cc_start: 0.7771 (pmm) cc_final: 0.7044 (ptp) REVERT: R 291 ASP cc_start: 0.7354 (m-30) cc_final: 0.6833 (m-30) REVERT: R 367 ASP cc_start: 0.7749 (t0) cc_final: 0.7325 (t0) REVERT: R 370 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8136 (tt0) REVERT: C 455 TYR cc_start: 0.7619 (m-80) cc_final: 0.7351 (m-10) REVERT: D 368 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5100 (tp) REVERT: D 562 TYR cc_start: 0.8481 (m-80) cc_final: 0.8255 (m-80) REVERT: E 364 LYS cc_start: 0.8163 (mttt) cc_final: 0.7552 (mtpp) REVERT: E 553 ASP cc_start: 0.8419 (p0) cc_final: 0.8097 (p0) REVERT: F 489 MET cc_start: 0.8811 (mmp) cc_final: 0.8423 (mmm) REVERT: F 493 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 405 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4147 (t80) REVERT: G 419 ASN cc_start: 0.9047 (m-40) cc_final: 0.8782 (m110) REVERT: H 453 ASP cc_start: 0.7665 (p0) cc_final: 0.7198 (p0) REVERT: H 463 GLN cc_start: 0.8409 (tt0) cc_final: 0.8160 (tt0) REVERT: K 500 TYR cc_start: 0.8605 (p90) cc_final: 0.8397 (p90) REVERT: K 534 TYR cc_start: 0.8366 (m-80) cc_final: 0.7781 (m-80) REVERT: L 378 VAL cc_start: 0.1575 (OUTLIER) cc_final: 0.1121 (p) REVERT: L 455 TYR cc_start: 0.5787 (m-80) cc_final: 0.5207 (m-80) REVERT: L 553 ASP cc_start: 0.7803 (t70) cc_final: 0.7531 (t0) REVERT: L 568 MET cc_start: 0.8333 (mmp) cc_final: 0.8119 (mmm) REVERT: J 46 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7550 (mtt-85) outliers start: 59 outliers final: 46 residues processed: 341 average time/residue: 0.3102 time to fit residues: 170.5282 Evaluate side-chains 332 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain C residue 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 368 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 416 ASP 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 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 170 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN C 385 GLN C 487 GLN C 545 ASN ** G 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21326 Z= 0.236 Angle : 0.608 10.454 29129 Z= 0.309 Chirality : 0.047 0.397 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.576 55.860 3082 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.71 % Allowed : 20.23 % 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: -0.22 (0.17), residues: 2600 helix: 0.32 (0.24), residues: 466 sheet: 0.25 (0.18), residues: 810 loop : -0.49 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 PHE 0.018 0.002 PHE L 424 TYR 0.023 0.002 TYR G 500 ARG 0.010 0.000 ARG F 491 *********************** 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 359 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 295 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8384 (mm-30) REVERT: R 278 HIS cc_start: 0.8578 (t-90) cc_final: 0.8225 (t70) REVERT: R 290 MET cc_start: 0.7834 (pmm) cc_final: 0.7617 (ptt) REVERT: R 367 ASP cc_start: 0.7647 (t0) cc_final: 0.7283 (t0) REVERT: R 370 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8096 (tt0) REVERT: B 415 GLU cc_start: 0.7980 (mp0) cc_final: 0.7495 (tm-30) REVERT: C 455 TYR cc_start: 0.7622 (m-80) cc_final: 0.7392 (m-10) REVERT: D 368 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.5046 (tp) REVERT: D 562 TYR cc_start: 0.8484 (m-80) cc_final: 0.8250 (m-80) REVERT: E 364 LYS cc_start: 0.8239 (mttt) cc_final: 0.7603 (mtpp) REVERT: E 553 ASP cc_start: 0.8375 (p0) cc_final: 0.7987 (p0) REVERT: F 489 MET cc_start: 0.8924 (mmp) cc_final: 0.8584 (mmm) REVERT: F 493 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7850 (tm-30) REVERT: G 405 PHE cc_start: 0.5059 (t80) cc_final: 0.4203 (t80) REVERT: G 419 ASN cc_start: 0.9046 (m-40) cc_final: 0.8779 (m110) REVERT: H 453 ASP cc_start: 0.7671 (p0) cc_final: 0.7218 (p0) REVERT: H 463 GLN cc_start: 0.8433 (tt0) cc_final: 0.8174 (tt0) REVERT: K 500 TYR cc_start: 0.8610 (p90) cc_final: 0.8354 (p90) REVERT: K 534 TYR cc_start: 0.8227 (m-80) cc_final: 0.7633 (m-80) REVERT: L 378 VAL cc_start: 0.1646 (OUTLIER) cc_final: 0.1187 (p) REVERT: L 490 GLN cc_start: 0.5841 (pt0) cc_final: 0.5503 (pt0) REVERT: L 553 ASP cc_start: 0.7857 (t70) cc_final: 0.7522 (t0) REVERT: J 46 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7607 (mtt-85) outliers start: 64 outliers final: 51 residues processed: 345 average time/residue: 0.3061 time to fit residues: 170.0379 Evaluate side-chains 329 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 348 LEU Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 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 471 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 385 GLN 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 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 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 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 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 227 optimal weight: 30.0000 chunk 239 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 140 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 chunk 220 optimal weight: 0.0170 chunk 231 optimal weight: 20.0000 overall best weight: 1.2198 ------------------------------------------------------------------------------- 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** C 385 GLN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21326 Z= 0.234 Angle : 0.614 10.503 29129 Z= 0.311 Chirality : 0.047 0.394 3415 Planarity : 0.004 0.057 3716 Dihedral : 5.506 57.937 3082 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.62 % Allowed : 20.82 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.17), residues: 2600 helix: 0.32 (0.24), residues: 469 sheet: 0.27 (0.18), residues: 800 loop : -0.50 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 362 HIS 0.011 0.001 HIS L 518 PHE 0.040 0.002 PHE G 485 TYR 0.024 0.002 TYR G 500 ARG 0.011 0.000 ARG F 491 *********************** 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 355 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 293 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8390 (mm-30) REVERT: R 295 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7062 (tp-100) REVERT: R 361 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8525 (mt-10) REVERT: R 367 ASP cc_start: 0.7667 (t0) cc_final: 0.7309 (t0) REVERT: R 370 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8119 (tt0) REVERT: B 415 GLU cc_start: 0.7927 (mp0) cc_final: 0.7501 (tm-30) REVERT: C 455 TYR cc_start: 0.7633 (m-80) cc_final: 0.7395 (m-10) REVERT: D 368 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.5009 (tp) REVERT: D 419 ASN cc_start: 0.8681 (m110) cc_final: 0.8449 (m110) REVERT: D 562 TYR cc_start: 0.8464 (m-80) cc_final: 0.8247 (m-80) REVERT: E 364 LYS cc_start: 0.8244 (mttt) cc_final: 0.7602 (mtpp) REVERT: E 553 ASP cc_start: 0.8377 (p0) cc_final: 0.7934 (p0) REVERT: F 489 MET cc_start: 0.8931 (mmp) cc_final: 0.8619 (mmm) REVERT: F 493 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7850 (tm-30) REVERT: G 405 PHE cc_start: 0.4988 (OUTLIER) cc_final: 0.4236 (t80) REVERT: G 419 ASN cc_start: 0.9039 (m-40) cc_final: 0.8776 (m110) REVERT: H 453 ASP cc_start: 0.7688 (p0) cc_final: 0.7217 (p0) REVERT: K 500 TYR cc_start: 0.8605 (p90) cc_final: 0.8386 (p90) REVERT: K 534 TYR cc_start: 0.8212 (m-80) cc_final: 0.7632 (m-80) REVERT: L 378 VAL cc_start: 0.1765 (OUTLIER) cc_final: 0.1283 (p) REVERT: L 553 ASP cc_start: 0.7910 (t70) cc_final: 0.7659 (t0) REVERT: J 46 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7572 (mtt-85) outliers start: 62 outliers final: 53 residues processed: 341 average time/residue: 0.2965 time to fit residues: 163.5361 Evaluate side-chains 336 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 348 LEU Chi-restraints excluded: chain R residue 374 SER 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 562 TYR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 385 GLN 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 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 348 PHE Chi-restraints excluded: chain G residue 405 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 414 CYS Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 chunk 171 optimal weight: 0.3980 chunk 258 optimal weight: 5.9990 chunk 237 optimal weight: 0.4980 chunk 205 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** C 385 GLN C 545 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN L 518 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21326 Z= 0.187 Angle : 0.613 10.847 29129 Z= 0.312 Chirality : 0.046 0.393 3415 Planarity : 0.005 0.117 3716 Dihedral : 5.360 59.592 3082 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.54 % Allowed : 20.91 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.23), residues: 469 sheet: 0.33 (0.18), residues: 800 loop : -0.49 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 362 HIS 0.012 0.001 HIS L 518 PHE 0.036 0.001 PHE G 485 TYR 0.029 0.002 TYR R 296 ARG 0.011 0.000 ARG F 491 ********************** 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 362 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 2.510 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 192 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8366 (mm-30) REVERT: R 295 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7231 (tm130) REVERT: R 367 ASP cc_start: 0.7609 (t0) cc_final: 0.7319 (t0) REVERT: R 370 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8118 (tt0) REVERT: C 358 PHE cc_start: 0.7926 (t80) cc_final: 0.7707 (t80) REVERT: C 455 TYR cc_start: 0.7576 (m-80) cc_final: 0.7350 (m-10) REVERT: D 368 LEU cc_start: 0.5271 (OUTLIER) cc_final: 0.5028 (tp) REVERT: D 419 ASN cc_start: 0.8690 (m110) cc_final: 0.8451 (m110) REVERT: E 364 LYS cc_start: 0.8220 (mttt) cc_final: 0.7684 (mtpp) REVERT: E 553 ASP cc_start: 0.8353 (p0) cc_final: 0.8028 (p0) REVERT: F 489 MET cc_start: 0.8910 (mmp) cc_final: 0.8612 (mmm) REVERT: F 493 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7884 (tm-30) REVERT: G 405 PHE cc_start: 0.4944 (t80) cc_final: 0.4230 (t80) REVERT: G 419 ASN cc_start: 0.9052 (m-40) cc_final: 0.8792 (m110) REVERT: H 453 ASP cc_start: 0.7726 (p0) cc_final: 0.7303 (p0) REVERT: K 534 TYR cc_start: 0.8157 (m-80) cc_final: 0.7678 (m-80) REVERT: L 378 VAL cc_start: 0.1737 (OUTLIER) cc_final: 0.1261 (p) REVERT: L 553 ASP cc_start: 0.7780 (t70) cc_final: 0.7398 (t0) REVERT: J 126 THR cc_start: 0.8624 (t) cc_final: 0.8293 (m) outliers start: 60 outliers final: 49 residues processed: 349 average time/residue: 0.2883 time to fit residues: 164.3612 Evaluate side-chains 337 residues out of total 2363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain R residue 315 PHE Chi-restraints excluded: chain R residue 348 LEU Chi-restraints excluded: chain R residue 376 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain F residue 548 THR 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 501 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain K residue 374 THR Chi-restraints excluded: chain K residue 376 ASP Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 416 ASP Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 570 ASP Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 211 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 GLN A 545 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.139632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.100371 restraints weight = 48518.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101595 restraints weight = 29179.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101983 restraints weight = 20856.324| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21326 Z= 0.210 Angle : 0.617 10.555 29129 Z= 0.313 Chirality : 0.046 0.400 3415 Planarity : 0.005 0.109 3716 Dihedral : 5.278 58.959 3082 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.45 % Allowed : 21.54 % Favored : 76.01 % 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: 0.28 (0.24), residues: 469 sheet: 0.37 (0.18), residues: 800 loop : -0.47 (0.18), residues: 1331 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 0.033 0.001 PHE G 485 TYR 0.024 0.002 TYR R 296 ARG 0.014 0.000 ARG F 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4270.34 seconds wall clock time: 79 minutes 39.26 seconds (4779.26 seconds total)