Starting phenix.real_space_refine on Mon Jul 6 15:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbp_27297/07_2026/8dbp_27297.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23265 2.51 5 N 6256 2.21 5 O 6902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 294 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36622 Number of models: 1 Model: "" Number of chains: 28 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "L" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "M" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "N" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "O" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "P" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "Q" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "R" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "S" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 545 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3863 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.45, per 1000 atoms: 0.20 Number of scatterers: 36622 At special positions: 0 Unit cell: (182.351, 224.432, 137.033, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 16 15.00 Mg 5 11.99 O 6902 8.00 N 6256 7.00 C 23265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8718 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 21 sheets defined 61.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.565A pdb=" N LEU I 8 " --> pdb=" O LEU I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.811A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.600A pdb=" N ALA I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 Processing helix chain 'J' and resid 45 through 77 removed outlier: 3.937A pdb=" N GLY J 58 " --> pdb=" O PHE J 54 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 42 Processing helix chain 'L' and resid 45 through 77 removed outlier: 3.682A pdb=" N GLN L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Proline residue: L 64 - end of helix Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.556A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 4.021A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 42 removed outlier: 3.607A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 61 removed outlier: 4.352A pdb=" N LEU N 48 " --> pdb=" O ASP N 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'O' and resid 4 through 42 removed outlier: 3.568A pdb=" N GLN O 42 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 77 removed outlier: 4.389A pdb=" N LEU O 48 " --> pdb=" O ASP O 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN O 52 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) Proline residue: O 64 - end of helix Processing helix chain 'P' and resid 4 through 42 removed outlier: 3.595A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN P 42 " --> pdb=" O GLY P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 removed outlier: 4.480A pdb=" N LEU P 48 " --> pdb=" O ASP P 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 77 removed outlier: 3.654A pdb=" N ALA P 77 " --> pdb=" O TYR P 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 40 Processing helix chain 'Q' and resid 45 through 61 removed outlier: 3.888A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 77 removed outlier: 3.583A pdb=" N GLY Q 69 " --> pdb=" O MET Q 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.593A pdb=" N TYR R 10 " --> pdb=" O MET R 6 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET R 11 " --> pdb=" O ASP R 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA R 14 " --> pdb=" O TYR R 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.754A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.546A pdb=" N ALA R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 42 removed outlier: 3.519A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA S 13 " --> pdb=" O LEU S 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.967A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 3.814A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.623A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.838A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 4.075A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.282A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 479 removed outlier: 3.875A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.529A pdb=" N MET A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.761A pdb=" N ILE B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.529A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.824A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 287 Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 288 through 299 removed outlier: 4.332A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.397A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 410 removed outlier: 3.736A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.771A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.532A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.623A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.750A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.735A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.513A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 290 through 299 removed outlier: 3.583A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.724A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 410 removed outlier: 3.515A pdb=" N LEU C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 4.014A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 196 through 197 No H-bonds generated for 'chain 'D' and resid 196 through 197' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.651A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.652A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.531A pdb=" N GLU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.569A pdb=" N LEU E 84 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.556A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 154 through 170 removed outlier: 3.524A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.571A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.735A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 4.019A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.665A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 305 through 313 removed outlier: 4.227A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 4.640A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 419 through 433 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 171 removed outlier: 3.676A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 5.181A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.566A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 313 removed outlier: 4.234A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 345 through 378 removed outlier: 5.607A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 400 removed outlier: 3.507A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'G' and resid 2 through 58 removed outlier: 3.591A pdb=" N SER G 41 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.595A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.627A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 210 through 281 removed outlier: 3.571A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 Processing helix chain 'W' and resid 6 through 21 removed outlier: 4.738A pdb=" N TYR W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 38 removed outlier: 3.582A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.601A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 64 Processing helix chain 'W' and resid 71 through 82 Processing helix chain 'W' and resid 83 through 86 removed outlier: 5.872A pdb=" N ASN W 86 " --> pdb=" O GLY W 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 83 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.739A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 163 through 169 Processing helix chain 'X' and resid 5 through 23 removed outlier: 3.605A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU X 16 " --> pdb=" O ILE X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.533A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS X 52 " --> pdb=" O GLU X 48 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 156 removed outlier: 3.865A pdb=" N LEU X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 25 removed outlier: 4.086A pdb=" N LEU Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 140 removed outlier: 4.089A pdb=" N GLU Y 39 " --> pdb=" O LYS Y 35 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS Y 100 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 156 Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.591A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.826A pdb=" N LEU a 59 " --> pdb=" O LEU a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.916A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.536A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 132 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 4.113A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 removed outlier: 3.767A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.558A pdb=" N MET a 215 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 3.704A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.862A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA a 267 " --> pdb=" O TYR a 263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 66 removed outlier: 3.692A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.759A pdb=" N GLY A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 109 current: chain 'A' and resid 221 through 226 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 221 through 226 current: chain 'A' and resid 322 through 331 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 331 current: chain 'A' and resid 374 through 375 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 35 removed outlier: 6.422A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 6.639A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'E' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 12 through 16 current: chain 'E' and resid 36 through 45 removed outlier: 6.829A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 55 current: chain 'W' and resid 135 through 142 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 142 current: chain 'W' and resid 157 through 162 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.594A pdb=" N TYR B 260 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 67 removed outlier: 3.875A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.616A pdb=" N VAL C 108 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.440A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.379A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.563A pdb=" N PHE D 139 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.632A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.148A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TYR E 297 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.765A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AB9, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.183A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 132 through 136 removed outlier: 8.044A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE G 169 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLN G 186 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER G 171 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE G 184 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYS G 173 " --> pdb=" O PRO G 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 206 through 208 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 208 current: chain 'H' and resid 16 through 26 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 31 through 34 current: chain 'H' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 64 current: chain 'H' and resid 75 through 80 Processing sheet with id=AC3, first strand: chain 'a' and resid 21 through 22 2237 hydrogen bonds defined for protein. 6519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10676 1.33 - 1.45: 4797 1.45 - 1.57: 21324 1.57 - 1.69: 26 1.69 - 1.81: 356 Bond restraints: 37179 Sorted by residual: bond pdb=" C4 ATP E 500 " pdb=" C5 ATP E 500 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.21e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.30e+01 bond pdb=" C5 ATP E 500 " pdb=" N7 ATP E 500 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.70e+01 ... (remaining 37174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 50043 4.68 - 9.35: 264 9.35 - 14.03: 7 14.03 - 18.70: 2 18.70 - 23.38: 6 Bond angle restraints: 50322 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.49 23.38 1.00e+00 1.00e+00 5.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.48 22.39 1.00e+00 1.00e+00 5.01e+02 angle pdb=" PB ATP E 500 " pdb=" O3B ATP E 500 " pdb=" PG ATP E 500 " ideal model delta sigma weight residual 139.87 119.42 20.45 1.00e+00 1.00e+00 4.18e+02 angle pdb=" PA ATP E 500 " pdb=" O3A ATP E 500 " pdb=" PB ATP E 500 " ideal model delta sigma weight residual 136.83 116.90 19.93 1.00e+00 1.00e+00 3.97e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.51 19.32 1.00e+00 1.00e+00 3.73e+02 ... (remaining 50317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.14: 21851 31.14 - 62.28: 543 62.28 - 93.41: 78 93.41 - 124.55: 2 124.55 - 155.69: 1 Dihedral angle restraints: 22475 sinusoidal: 8843 harmonic: 13632 Sorted by residual: dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 144.31 155.69 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 -179.15 119.15 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 52.77 -112.77 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 22472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4904 0.084 - 0.168: 873 0.168 - 0.251: 61 0.251 - 0.335: 11 0.335 - 0.419: 3 Chirality restraints: 5852 Sorted by residual: chirality pdb=" CA ASP Y 53 " pdb=" N ASP Y 53 " pdb=" C ASP Y 53 " pdb=" CB ASP Y 53 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB VAL a 29 " pdb=" CA VAL a 29 " pdb=" CG1 VAL a 29 " pdb=" CG2 VAL a 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ASP C 262 " pdb=" N ASP C 262 " pdb=" C ASP C 262 " pdb=" CB ASP C 262 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5849 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 164 " -0.169 9.50e-02 1.11e+02 9.29e-02 3.96e+01 pdb=" NE ARG C 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 164 " -0.102 2.00e-02 2.50e+03 pdb=" NH1 ARG C 164 " 0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG C 164 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 41 " -0.133 9.50e-02 1.11e+02 7.69e-02 3.15e+01 pdb=" NE ARG M 41 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG M 41 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG M 41 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG M 41 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 52 " 0.128 9.50e-02 1.11e+02 7.36e-02 2.84e+01 pdb=" NE ARG F 52 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 52 " 0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG F 52 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG F 52 " -0.025 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.99: 19216 2.99 - 3.63: 54245 3.63 - 4.26: 83669 4.26 - 4.90: 142104 Nonbonded interactions: 299254 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.714 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.719 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.774 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.801 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.888 2.170 ... (remaining 299249 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 2 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 601)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.690 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.010 0.085 37179 Z= 0.489 Angle : 1.204 23.378 50322 Z= 0.768 Chirality : 0.062 0.419 5852 Planarity : 0.008 0.101 6491 Dihedral : 14.311 155.690 13757 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.38 % Favored : 97.52 % Rotamer: Outliers : 1.39 % Allowed : 7.29 % Favored : 91.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.11), residues: 4756 helix: -0.72 (0.09), residues: 2561 sheet: -0.20 (0.20), residues: 545 loop : -0.69 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.104 0.013 ARG C 164 TYR 0.052 0.008 TYR E 435 PHE 0.037 0.004 PHE G 125 TRP 0.053 0.004 TRP G 203 HIS 0.017 0.003 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.01001 / 0.49 (37179) covalent geometry : angle 1.20364 / 0.77 (50322) hydrogen bonds : bond 0.22095 / 14.80 ( 2237) hydrogen bonds : angle 7.93105 / 5.77 ( 6519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 489 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 37 GLU cc_start: 0.6790 (tt0) cc_final: 0.6576 (mt-10) REVERT: I 66 ILE cc_start: 0.7263 (mt) cc_final: 0.6929 (mt) REVERT: J 75 MET cc_start: 0.6058 (tmm) cc_final: 0.5845 (tmm) REVERT: L 8 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6164 (mp) REVERT: L 65 MET cc_start: 0.6493 (mmt) cc_final: 0.6232 (mmm) REVERT: L 68 VAL cc_start: 0.4682 (t) cc_final: 0.4116 (m) REVERT: M 17 MET cc_start: 0.6990 (mmm) cc_final: 0.6746 (tmm) REVERT: M 28 ILE cc_start: 0.6855 (mt) cc_final: 0.6578 (mm) REVERT: M 41 ARG cc_start: 0.6601 (mtm110) cc_final: 0.6267 (ptp-170) REVERT: N 54 PHE cc_start: 0.7763 (m-80) cc_final: 0.7363 (t80) REVERT: O 17 MET cc_start: 0.0147 (mpp) cc_final: -0.0756 (mmt) REVERT: O 54 PHE cc_start: 0.5399 (m-80) cc_final: 0.4730 (p90) REVERT: O 57 MET cc_start: 0.4811 (tmm) cc_final: 0.4539 (tpp) REVERT: P 16 MET cc_start: 0.6137 (ttp) cc_final: 0.5898 (tmm) REVERT: P 17 MET cc_start: 0.6271 (tmm) cc_final: 0.5862 (tpt) REVERT: P 37 GLU cc_start: 0.8980 (tt0) cc_final: 0.8201 (tt0) REVERT: P 54 PHE cc_start: 0.6767 (m-10) cc_final: 0.6134 (t80) REVERT: Q 17 MET cc_start: 0.4685 (mmm) cc_final: 0.2324 (tpp) REVERT: Q 37 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6529 (mm-30) REVERT: Q 68 VAL cc_start: 0.7502 (m) cc_final: 0.7171 (p) REVERT: R 6 MET cc_start: 0.4386 (ptt) cc_final: 0.4164 (tmm) REVERT: A 48 MET cc_start: 0.8578 (ptp) cc_final: 0.8375 (ptp) REVERT: A 52 MET cc_start: 0.7713 (mtp) cc_final: 0.7503 (mtp) REVERT: B 48 MET cc_start: 0.7847 (ptp) cc_final: 0.7625 (ptm) REVERT: C 262 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: E 56 MET cc_start: 0.9314 (mmp) cc_final: 0.9075 (mmt) REVERT: F 56 MET cc_start: 0.9172 (mmm) cc_final: 0.8955 (mmt) REVERT: F 88 MET cc_start: 0.8519 (mtm) cc_final: 0.8246 (mtp) REVERT: G 48 MET cc_start: 0.9021 (ttm) cc_final: 0.8705 (ttp) REVERT: H 25 VAL cc_start: 0.7854 (t) cc_final: 0.7474 (m) REVERT: H 29 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7321 (mt-10) REVERT: X 22 MET cc_start: 0.6152 (ttm) cc_final: 0.5867 (tpt) outliers start: 53 outliers final: 11 residues processed: 535 average time/residue: 0.2410 time to fit residues: 203.5232 Evaluate side-chains 293 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain Y residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 52 GLN J 3 ASN M 52 GLN N 5 ASN O 52 GLN P 52 GLN R 52 GLN S 52 GLN A 65 ASN A 344 ASN A 399 GLN A 420 GLN B 2 GLN B 20 ASN B 42 HIS B 58 ASN B 147 GLN B 186 GLN B 484 GLN C 420 GLN C 511 GLN D 353 HIS D 361 GLN D 397 GLN E 197 ASN F 32 GLN F 365 GLN G 131 ASN ** G 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 75 ASN ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 ASN a 181 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.070638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048677 restraints weight = 189708.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049284 restraints weight = 97157.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.049303 restraints weight = 59684.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049419 restraints weight = 54271.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049513 restraints weight = 47274.699| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 37179 Z= 0.176 Angle : 0.690 10.121 50322 Z= 0.364 Chirality : 0.044 0.191 5852 Planarity : 0.005 0.056 6491 Dihedral : 6.594 153.033 5205 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.16 % Favored : 98.82 % Rotamer: Outliers : 1.87 % Allowed : 9.89 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 4756 helix: 1.09 (0.10), residues: 2615 sheet: 0.29 (0.22), residues: 488 loop : -0.27 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 49 TYR 0.041 0.002 TYR a 263 PHE 0.024 0.002 PHE C 406 TRP 0.016 0.002 TRP G 203 HIS 0.010 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (37179) covalent geometry : angle 0.68980 / 0.36 (50322) hydrogen bonds : bond 0.06464 / 4.33 ( 2237) hydrogen bonds : angle 4.92981 / 3.62 ( 6519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 326 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 44 ASP cc_start: 0.7765 (p0) cc_final: 0.7122 (p0) REVERT: L 6 MET cc_start: 0.4853 (mtp) cc_final: 0.4482 (tmm) REVERT: L 68 VAL cc_start: 0.4863 (t) cc_final: 0.4495 (m) REVERT: M 6 MET cc_start: 0.2592 (OUTLIER) cc_final: 0.2268 (mmm) REVERT: M 16 MET cc_start: 0.4940 (ptm) cc_final: 0.4646 (ptm) REVERT: N 54 PHE cc_start: 0.7750 (m-80) cc_final: 0.7271 (t80) REVERT: O 17 MET cc_start: -0.0002 (mpp) cc_final: -0.0764 (mmt) REVERT: O 54 PHE cc_start: 0.5865 (m-80) cc_final: 0.5051 (t80) REVERT: P 16 MET cc_start: 0.6009 (ttp) cc_final: 0.5656 (tmm) REVERT: P 17 MET cc_start: 0.6048 (tmm) cc_final: 0.5784 (tpt) REVERT: R 6 MET cc_start: 0.4359 (ptt) cc_final: 0.3172 (tpp) REVERT: S 65 MET cc_start: 0.2827 (mtt) cc_final: 0.2392 (mmm) REVERT: B 48 MET cc_start: 0.7991 (ptp) cc_final: 0.7651 (ptm) REVERT: C 262 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: C 425 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: E 379 MET cc_start: 0.8039 (ttp) cc_final: 0.7809 (tmm) REVERT: F 56 MET cc_start: 0.9267 (mmm) cc_final: 0.8945 (mmt) REVERT: F 387 LYS cc_start: 0.5669 (OUTLIER) cc_final: 0.5361 (mptt) REVERT: F 431 MET cc_start: 0.8474 (mmm) cc_final: 0.8232 (mmm) REVERT: F 458 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7586 (mtmm) REVERT: G 116 MET cc_start: 0.9188 (mmm) cc_final: 0.8868 (mmm) REVERT: G 155 MET cc_start: 0.9235 (mmt) cc_final: 0.8942 (mmt) REVERT: W 90 ASP cc_start: 0.8483 (t0) cc_final: 0.8257 (t0) REVERT: W 147 MET cc_start: 0.9071 (mtm) cc_final: 0.8564 (mmm) REVERT: W 157 MET cc_start: 0.7635 (mmm) cc_final: 0.7271 (mmm) REVERT: X 85 GLN cc_start: 0.8961 (mt0) cc_final: 0.8603 (mt0) REVERT: X 113 ARG cc_start: 0.8882 (mmm160) cc_final: 0.8656 (tpt170) REVERT: Y 96 GLN cc_start: 0.9336 (tm-30) cc_final: 0.9100 (mp10) REVERT: a 89 SER cc_start: 0.8419 (m) cc_final: 0.8041 (p) REVERT: a 118 MET cc_start: 0.7636 (mtm) cc_final: 0.7429 (ptp) outliers start: 71 outliers final: 24 residues processed: 379 average time/residue: 0.2155 time to fit residues: 137.1097 Evaluate side-chains 294 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain M residue 6 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain Y residue 114 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 316 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 456 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 257 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 418 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 53 optimal weight: 0.0050 chunk 92 optimal weight: 8.9990 overall best weight: 3.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN B 26 HIS E 121 ASN H 14 GLN H 72 GLN X 96 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.068693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045834 restraints weight = 191387.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047476 restraints weight = 94065.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.047152 restraints weight = 52290.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047536 restraints weight = 45314.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.047606 restraints weight = 40714.179| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37179 Z= 0.216 Angle : 0.664 9.830 50322 Z= 0.344 Chirality : 0.043 0.165 5852 Planarity : 0.004 0.048 6491 Dihedral : 6.057 160.492 5194 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.66 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 10.78 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 4756 helix: 1.51 (0.10), residues: 2611 sheet: 0.29 (0.21), residues: 522 loop : -0.27 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 49 TYR 0.023 0.002 TYR a 164 PHE 0.022 0.002 PHE C 406 TRP 0.014 0.001 TRP a 232 HIS 0.009 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (37179) covalent geometry : angle 0.66379 / 0.34 (50322) hydrogen bonds : bond 0.05868 / 3.92 ( 2237) hydrogen bonds : angle 4.67148 / 3.44 ( 6519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 280 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 17 MET cc_start: 0.3327 (mtp) cc_final: 0.2549 (tpp) REVERT: L 6 MET cc_start: 0.4917 (mtp) cc_final: 0.4511 (tmm) REVERT: L 68 VAL cc_start: 0.4850 (t) cc_final: 0.4588 (m) REVERT: M 6 MET cc_start: 0.2342 (OUTLIER) cc_final: 0.2041 (mmm) REVERT: N 54 PHE cc_start: 0.7786 (m-80) cc_final: 0.7320 (t80) REVERT: O 17 MET cc_start: 0.0035 (mpp) cc_final: -0.0728 (tpt) REVERT: O 54 PHE cc_start: 0.6203 (m-10) cc_final: 0.5257 (t80) REVERT: P 11 MET cc_start: 0.7080 (tpt) cc_final: 0.6396 (tmm) REVERT: R 6 MET cc_start: 0.4462 (ptt) cc_final: 0.3984 (tmm) REVERT: R 17 MET cc_start: 0.3165 (tpt) cc_final: 0.2964 (tpt) REVERT: S 55 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7109 (pt) REVERT: S 57 MET cc_start: 0.5157 (tmm) cc_final: 0.4796 (tpp) REVERT: S 65 MET cc_start: 0.3062 (mtt) cc_final: 0.2493 (mmm) REVERT: A 95 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9024 (tp) REVERT: A 386 MET cc_start: 0.9060 (mmt) cc_final: 0.8848 (mmm) REVERT: B 48 MET cc_start: 0.8333 (ptp) cc_final: 0.8093 (ptm) REVERT: C 425 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: D 136 MET cc_start: 0.9186 (mmm) cc_final: 0.8779 (mmm) REVERT: F 56 MET cc_start: 0.9219 (mmm) cc_final: 0.8464 (mmt) REVERT: F 431 MET cc_start: 0.8494 (mmm) cc_final: 0.8284 (mmm) REVERT: G 116 MET cc_start: 0.9259 (mmm) cc_final: 0.8844 (mmm) REVERT: G 243 MET cc_start: 0.8753 (ttp) cc_final: 0.8528 (ttt) REVERT: W 30 MET cc_start: 0.8488 (ptp) cc_final: 0.8262 (ptp) REVERT: W 90 ASP cc_start: 0.8472 (t0) cc_final: 0.8132 (t0) REVERT: X 49 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7424 (ptt-90) REVERT: X 85 GLN cc_start: 0.8955 (mt0) cc_final: 0.8663 (mt0) REVERT: Y 117 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.7841 (ttp80) REVERT: a 93 MET cc_start: 0.8344 (mpp) cc_final: 0.6637 (tpp) REVERT: a 118 MET cc_start: 0.7742 (mtm) cc_final: 0.7422 (ptp) REVERT: a 245 HIS cc_start: 0.1045 (OUTLIER) cc_final: 0.0692 (t70) REVERT: a 257 MET cc_start: 0.9178 (tmm) cc_final: 0.8939 (ppp) outliers start: 84 outliers final: 33 residues processed: 348 average time/residue: 0.2095 time to fit residues: 123.5296 Evaluate side-chains 291 residues out of total 3805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 6 MET Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain F residue 0 MET Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain W residue 96 ILE Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 48 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain a residue 245 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0178 > 50: distance: 11 - 77: 3.456 distance: 77 - 78: 8.534 distance: 78 - 79: 14.119 distance: 78 - 81: 10.173 distance: 79 - 80: 18.254 distance: 79 - 85: 15.261 distance: 81 - 82: 5.155 distance: 82 - 83: 15.933 distance: 82 - 84: 10.435 distance: 85 - 86: 13.987 distance: 86 - 87: 16.357 distance: 86 - 89: 16.448 distance: 87 - 88: 26.479 distance: 87 - 93: 26.800 distance: 89 - 90: 24.520 distance: 90 - 91: 21.349 distance: 90 - 92: 5.760 distance: 93 - 94: 9.798 distance: 94 - 95: 17.658 distance: 94 - 97: 14.742 distance: 95 - 96: 18.326 distance: 95 - 101: 8.769 distance: 96 - 125: 15.638 distance: 98 - 99: 25.635 distance: 98 - 100: 28.399 distance: 101 - 102: 17.163 distance: 102 - 103: 9.078 distance: 102 - 105: 12.075 distance: 103 - 104: 6.170 distance: 103 - 107: 5.853 distance: 104 - 130: 9.884 distance: 105 - 106: 10.147 distance: 107 - 108: 5.763 distance: 108 - 109: 6.066 distance: 108 - 111: 9.111 distance: 109 - 110: 10.706 distance: 109 - 116: 10.309 distance: 110 - 137: 15.977 distance: 111 - 112: 12.129 distance: 112 - 113: 8.987 distance: 113 - 114: 14.261 distance: 114 - 115: 15.992 distance: 116 - 117: 4.703 distance: 117 - 118: 9.644 distance: 117 - 120: 6.469 distance: 118 - 119: 5.759 distance: 118 - 125: 3.179 distance: 119 - 142: 19.584 distance: 120 - 121: 12.043 distance: 121 - 122: 12.219 distance: 122 - 123: 7.524 distance: 122 - 124: 20.520 distance: 125 - 126: 11.651 distance: 126 - 127: 22.242 distance: 126 - 129: 6.474 distance: 127 - 128: 19.430 distance: 127 - 130: 27.834 distance: 128 - 154: 14.326 distance: 130 - 131: 8.706 distance: 131 - 132: 8.775 distance: 132 - 133: 10.348 distance: 132 - 137: 5.614 distance: 133 - 163: 12.324 distance: 134 - 135: 8.292 distance: 134 - 136: 23.652 distance: 137 - 138: 7.897 distance: 138 - 139: 11.896 distance: 138 - 141: 8.916 distance: 139 - 140: 9.029 distance: 139 - 142: 7.367 distance: 140 - 171: 11.365 distance: 142 - 143: 4.685 distance: 143 - 144: 6.461 distance: 143 - 146: 9.076 distance: 144 - 145: 7.459 distance: 145 - 179: 11.725 distance: 146 - 147: 7.030 distance: 147 - 148: 5.329 distance: 147 - 149: 16.206 distance: 148 - 150: 7.815 distance: 150 - 152: 11.360 distance: 151 - 152: 9.473 distance: 152 - 153: 7.614