Starting phenix.real_space_refine on Sat Mar 7 06:30:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r0y_4700/03_2026/6r0y_4700.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r0y_4700/03_2026/6r0y_4700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r0y_4700/03_2026/6r0y_4700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r0y_4700/03_2026/6r0y_4700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r0y_4700/03_2026/6r0y_4700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r0y_4700/03_2026/6r0y_4700.map" } resolution = 3.9 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= 0.004 sd= 0.016 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 4 5.49 5 Mg 1 5.21 5 S 103 5.16 5 C 25034 2.51 5 N 7293 2.21 5 O 7734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40169 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3609 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 434} Chain: "E" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3618 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 435} Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3608 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 434} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 808 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1441 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'ASP:plan': 20, 'PHE:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 35, 'GLU:plan': 26, 'GLN:plan1': 12, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 566 Chain: "N" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 3190 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2030 Unresolved non-hydrogen angles: 2628 Unresolved non-hydrogen dihedrals: 1714 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLU:plan': 56, 'ARG:plan': 37, 'GLN:plan1': 17, 'HIS:plan': 21, 'TYR:plan': 18, 'TRP:plan': 12, 'PHE:plan': 33, 'ASP:plan': 12, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 1071 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 356 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 347 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "B" 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} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.72, per 1000 atoms: 0.22 Number of scatterers: 40169 At special positions: 0 Unit cell: (152.985, 150.815, 254.975, 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 103 16.00 P 4 15.00 Mg 1 11.99 O 7734 8.00 N 7293 7.00 C 25034 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10536 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 42 sheets defined 56.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.531A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.723A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.284A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.514A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.596A pdb=" N PHE A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 5.545A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 508 through 531 Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.200A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.608A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 259 through 269 removed outlier: 4.924A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 297 through 316 removed outlier: 4.470A pdb=" N ALA B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.865A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.583A pdb=" N GLY B 349 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 352 No H-bonds generated for 'chain 'B' and resid 351 through 352' Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.154A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.528A pdb=" N GLY B 426 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 427 " --> pdb=" O TRP B 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 427' Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 446 through 471 removed outlier: 4.733A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.728A pdb=" N LEU B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 532 removed outlier: 3.517A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 551 Processing helix chain 'B' and resid 558 through 573 Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.517A pdb=" N ILE C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.714A pdb=" N VAL C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.679A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 295 through 315 removed outlier: 5.715A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.537A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 431 through 434 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 464 removed outlier: 3.678A pdb=" N LEU C 450 " --> pdb=" O ASP C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.992A pdb=" N VAL C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 480 through 494 Processing helix chain 'C' and resid 508 through 530 Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 558 through 577 removed outlier: 4.929A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.547A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.606A pdb=" N SER D 178 " --> pdb=" O PRO D 175 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 179' Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.906A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS D 264 " --> pdb=" O MET D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 4.264A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 283' Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.714A pdb=" N LYS D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.728A pdb=" N MET D 362 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN D 363 " --> pdb=" O ARG D 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 363' Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.520A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 422 removed outlier: 3.878A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 462 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 227 through 249 removed outlier: 3.746A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 279 through 283 removed outlier: 4.104A pdb=" N GLY E 282 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.739A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.804A pdb=" N ILE E 348 " --> pdb=" O HIS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 365 removed outlier: 4.398A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.855A pdb=" N ASP E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE E 392 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.914A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.644A pdb=" N ALA F 171 " --> pdb=" O ILE F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 removed outlier: 4.161A pdb=" N THR F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 248 removed outlier: 3.981A pdb=" N ARG F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 259 through 270 removed outlier: 3.540A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 4.178A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 331 Processing helix chain 'F' and resid 340 through 346 removed outlier: 4.043A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 397 removed outlier: 3.817A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.564A pdb=" N ARG F 409 " --> pdb=" O THR F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 462 removed outlier: 3.873A pdb=" N ILE F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 70 removed outlier: 3.676A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.863A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 169 Processing helix chain 'G' and resid 169 through 203 removed outlier: 4.081A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.589A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 55 through 62 removed outlier: 3.973A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 19 through 105 removed outlier: 4.014A pdb=" N LYS I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 119 Processing helix chain 'J' and resid 3 through 94 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 99 through 114 removed outlier: 4.635A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 133 Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 167 through 187 removed outlier: 5.935A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 106 removed outlier: 3.923A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'L' and resid 3 through 91 removed outlier: 4.020A pdb=" N GLU L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.538A pdb=" N LEU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 188 removed outlier: 5.450A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 18 removed outlier: 4.106A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 28 removed outlier: 3.608A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 42 Processing helix chain 'M' and resid 43 through 48 Processing helix chain 'M' and resid 53 through 71 removed outlier: 4.082A pdb=" N ASP M 71 " --> pdb=" O LYS M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 86 Processing helix chain 'M' and resid 88 through 106 removed outlier: 4.473A pdb=" N ASP M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 129 removed outlier: 4.134A pdb=" N TRP M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU M 129 " --> pdb=" O ARG M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 145 through 154 removed outlier: 3.773A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 157 No H-bonds generated for 'chain 'M' and resid 155 through 157' Processing helix chain 'M' and resid 161 through 182 Processing helix chain 'M' and resid 185 through 207 Processing helix chain 'M' and resid 213 through 218 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 244 Processing helix chain 'M' and resid 258 through 275 Processing helix chain 'M' and resid 276 through 279 removed outlier: 3.618A pdb=" N ASP M 279 " --> pdb=" O GLY M 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 276 through 279' Processing helix chain 'M' and resid 283 through 310 Processing helix chain 'N' and resid 13 through 27 Processing helix chain 'N' and resid 46 through 71 Processing helix chain 'N' and resid 83 through 116 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 118 through 129 Processing helix chain 'N' and resid 149 through 160 removed outlier: 3.562A pdb=" N VAL N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 198 Processing helix chain 'N' and resid 212 through 268 Proline residue: N 228 - end of helix removed outlier: 5.642A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 285 No H-bonds generated for 'chain 'N' and resid 283 through 285' Processing helix chain 'N' and resid 286 through 296 removed outlier: 3.526A pdb=" N ARG N 296 " --> pdb=" O GLU N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 327 through 329 No H-bonds generated for 'chain 'N' and resid 327 through 329' Processing helix chain 'N' and resid 330 through 336 Processing helix chain 'N' and resid 349 through 363 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 386 Processing helix chain 'N' and resid 399 through 425 removed outlier: 3.685A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 489 Processing helix chain 'N' and resid 491 through 516 Processing helix chain 'N' and resid 524 through 543 Processing helix chain 'N' and resid 547 through 560 removed outlier: 3.932A pdb=" N ILE N 551 " --> pdb=" O MET N 547 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 587 removed outlier: 3.958A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 593 through 632 removed outlier: 4.611A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 3.849A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 4.211A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 61 Processing helix chain 'O' and resid 63 through 80 Processing helix chain 'P' and resid 10 through 48 removed outlier: 3.813A pdb=" N LEU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 removed outlier: 3.518A pdb=" N ALA P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 79 removed outlier: 4.173A pdb=" N VAL P 66 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 48 removed outlier: 4.150A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 removed outlier: 3.527A pdb=" N ALA Q 55 " --> pdb=" O ASN Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 79 removed outlier: 4.442A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 48 removed outlier: 3.982A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 removed outlier: 3.649A pdb=" N LEU R 56 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 11 through 48 removed outlier: 4.227A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 62 through 80 removed outlier: 4.356A pdb=" N VAL S 66 " --> pdb=" O PRO S 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 48 removed outlier: 3.918A pdb=" N ALA T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 63 through 80 Processing helix chain 'U' and resid 11 through 48 removed outlier: 4.056A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 63 through 80 Processing helix chain 'V' and resid 10 through 48 removed outlier: 4.117A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 62 through 80 removed outlier: 4.423A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 48 removed outlier: 4.087A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 63 through 80 Processing helix chain 'X' and resid 10 through 48 removed outlier: 4.043A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 51 No H-bonds generated for 'chain 'X' and resid 49 through 51' Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 80 Processing helix chain 'Y' and resid 11 through 46 removed outlier: 4.114A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 63 through 79 Processing helix chain 'Z' and resid 9 through 48 removed outlier: 3.878A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 63 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 5.366A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.289A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 320 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 381 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 322 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 383 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA A 324 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.289A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 320 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 381 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 322 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 383 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA A 324 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 224 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.787A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.406A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 9 removed outlier: 6.514A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.606A pdb=" N GLY B 82 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA B 289 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 249 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 255 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 320 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B 381 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 322 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 383 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 324 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL B 378 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.606A pdb=" N GLY B 82 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA B 289 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 249 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 255 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 320 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B 381 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 322 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 383 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 324 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB4, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.823A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.740A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 63 through 65 removed outlier: 6.962A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.439A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AC2, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.607A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 139 removed outlier: 3.985A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AC5, first strand: chain 'D' and resid 14 through 15 removed outlier: 6.854A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 32 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AC7, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.266A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA D 188 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 124 through 125 removed outlier: 4.533A pdb=" N VAL D 300 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.968A pdb=" N LYS J 119 " --> pdb=" O GLU J 141 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN J 143 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU J 121 " --> pdb=" O GLN J 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.333A pdb=" N ILE E 11 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU E 22 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 32 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AD3, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.690A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 18 through 22 removed outlier: 7.164A pdb=" N TYR F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL F 50 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AD6, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.512A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 129 through 130 removed outlier: 4.582A pdb=" N GLN F 129 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 218 through 219 removed outlier: 6.648A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 4 removed outlier: 7.699A pdb=" N ILE H 4 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 141 through 144 Processing sheet with id=AE3, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.425A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.425A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 140 through 145 Processing sheet with id=AE6, first strand: chain 'N' and resid 389 through 391 2689 hydrogen bonds defined for protein. 7863 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: 9.15 Time building geometry restraints manager: 4.08 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: 11677 1.33 - 1.45: 6341 1.45 - 1.57: 22492 1.57 - 1.69: 6 1.69 - 1.81: 194 Bond restraints: 40710 Sorted by residual: bond pdb=" C GLY F 16 " pdb=" N PRO F 17 " ideal model delta sigma weight residual 1.331 1.306 0.025 7.90e-03 1.60e+04 1.04e+01 bond pdb=" C ASP F 353 " pdb=" N PRO F 354 " ideal model delta sigma weight residual 1.331 1.310 0.021 7.90e-03 1.60e+04 7.28e+00 bond pdb=" CB ASP D 327 " pdb=" CG ASP D 327 " ideal model delta sigma weight residual 1.516 1.454 0.062 2.50e-02 1.60e+03 6.20e+00 bond pdb=" CA MET D 194 " pdb=" CB MET D 194 " ideal model delta sigma weight residual 1.539 1.426 0.114 4.88e-02 4.20e+02 5.45e+00 bond pdb=" CG1 ILE D 392 " pdb=" CD1 ILE D 392 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.32e+00 ... (remaining 40705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 54195 3.17 - 6.33: 1002 6.33 - 9.50: 118 9.50 - 12.67: 26 12.67 - 15.83: 5 Bond angle restraints: 55346 Sorted by residual: angle pdb=" C THR E 197 " pdb=" N GLN E 198 " pdb=" CA GLN E 198 " ideal model delta sigma weight residual 121.54 133.20 -11.66 1.91e+00 2.74e-01 3.73e+01 angle pdb=" N ILE N 454 " pdb=" CA ILE N 454 " pdb=" C ILE N 454 " ideal model delta sigma weight residual 113.42 106.99 6.43 1.17e+00 7.31e-01 3.02e+01 angle pdb=" C ILE F 106 " pdb=" N THR F 107 " pdb=" CA THR F 107 " ideal model delta sigma weight residual 121.80 134.96 -13.16 2.44e+00 1.68e-01 2.91e+01 angle pdb=" C THR D 258 " pdb=" N ASP D 259 " pdb=" CA ASP D 259 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LYS E 149 " pdb=" N LEU E 150 " pdb=" CA LEU E 150 " ideal model delta sigma weight residual 122.31 110.75 11.56 2.34e+00 1.83e-01 2.44e+01 ... (remaining 55341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 24085 27.88 - 55.75: 378 55.75 - 83.63: 12 83.63 - 111.50: 1 111.50 - 139.38: 2 Dihedral angle restraints: 24478 sinusoidal: 7991 harmonic: 16487 Sorted by residual: dihedral pdb=" CA ASP H 85 " pdb=" C ASP H 85 " pdb=" N VAL H 86 " pdb=" CA VAL H 86 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA VAL N 301 " pdb=" C VAL N 301 " pdb=" N VAL N 302 " pdb=" CA VAL N 302 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA ARG E 345 " pdb=" C ARG E 345 " pdb=" N LYS E 346 " pdb=" CA LYS E 346 " ideal model delta harmonic sigma weight residual 180.00 145.66 34.34 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 24475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5793 0.099 - 0.198: 593 0.198 - 0.296: 25 0.296 - 0.395: 4 0.395 - 0.494: 1 Chirality restraints: 6416 Sorted by residual: chirality pdb=" CB ILE C 454 " pdb=" CA ILE C 454 " pdb=" CG1 ILE C 454 " pdb=" CG2 ILE C 454 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE F 106 " pdb=" CA ILE F 106 " pdb=" CG1 ILE F 106 " pdb=" CG2 ILE F 106 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 6413 not shown) Planarity restraints: 7460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 279 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO A 280 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 311 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO D 312 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 407 " -0.021 2.00e-02 2.50e+03 1.91e-02 9.14e+00 pdb=" CG TRP C 407 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 407 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 407 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 407 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 407 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 407 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 407 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 407 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 407 " -0.001 2.00e-02 2.50e+03 ... (remaining 7457 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2076 2.71 - 3.26: 39218 3.26 - 3.81: 65406 3.81 - 4.35: 74763 4.35 - 4.90: 129913 Nonbonded interactions: 311376 Sorted by model distance: nonbonded pdb=" OG1 THR B 235 " pdb="MG MG B 601 " model vdw 2.169 2.170 nonbonded pdb=" O LYS D 149 " pdb=" OG1 THR D 333 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP D 34 " pdb=" OG SER D 74 " model vdw 2.231 3.040 nonbonded pdb=" O ARG D 274 " pdb=" O2' ADP D 501 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR C 291 " pdb=" OD1 ASN C 293 " model vdw 2.267 3.040 ... (remaining 311371 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' selection = (chain 'B' and resid 1 through 577) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 464) selection = (chain 'E' and resid 5 through 464) selection = (chain 'F' and resid 5 through 464) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 2 through 187) } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 0.190 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.760 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.009 0.114 40710 Z= 0.370 Angle : 1.078 15.832 55346 Z= 0.579 Chirality : 0.060 0.494 6416 Planarity : 0.008 0.092 7460 Dihedral : 10.271 139.381 13942 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.25 % Favored : 92.72 % Rotamer: Outliers : 0.31 % Allowed : 4.78 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.22 (0.08), residues: 5793 helix: -2.33 (0.06), residues: 3110 sheet: -2.85 (0.18), residues: 585 loop : -3.29 (0.11), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 440 TYR 0.036 0.003 TYR D 383 PHE 0.036 0.003 PHE A 269 TRP 0.050 0.005 TRP C 407 HIS 0.016 0.004 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00872 (40710) covalent geometry : angle 1.07804 (55346) hydrogen bonds : bond 0.09763 ( 2671) hydrogen bonds : angle 6.10757 ( 7863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1040 time to evaluate : 1.391 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.9123 (t70) cc_final: 0.8907 (p0) REVERT: A 130 ARG cc_start: 0.8773 (pmm150) cc_final: 0.8552 (ptp90) REVERT: A 200 ASP cc_start: 0.8683 (p0) cc_final: 0.8482 (m-30) REVERT: A 202 ASN cc_start: 0.9331 (t160) cc_final: 0.9094 (t0) REVERT: A 213 ASP cc_start: 0.9215 (p0) cc_final: 0.8972 (p0) REVERT: A 300 GLU cc_start: 0.9259 (tt0) cc_final: 0.8777 (pt0) REVERT: A 336 GLU cc_start: 0.9347 (tm-30) cc_final: 0.9068 (tm-30) REVERT: A 361 PHE cc_start: 0.9094 (t80) cc_final: 0.8869 (t80) REVERT: A 509 MET cc_start: 0.8366 (mmm) cc_final: 0.8064 (mmm) REVERT: A 516 MET cc_start: 0.8435 (mtm) cc_final: 0.8206 (ptp) REVERT: A 524 LYS cc_start: 0.8728 (tttp) cc_final: 0.8315 (mtmm) REVERT: B 36 VAL cc_start: 0.9284 (t) cc_final: 0.9083 (p) REVERT: B 114 GLU cc_start: 0.8253 (pt0) cc_final: 0.7920 (mp0) REVERT: B 133 MET cc_start: 0.8801 (ttt) cc_final: 0.8546 (mmt) REVERT: B 213 ASP cc_start: 0.9240 (m-30) cc_final: 0.8672 (t0) REVERT: B 220 MET cc_start: 0.8494 (tpt) cc_final: 0.7943 (tpp) REVERT: B 248 ASP cc_start: 0.9199 (m-30) cc_final: 0.8684 (t0) REVERT: B 263 THR cc_start: 0.9380 (m) cc_final: 0.9041 (p) REVERT: B 337 ILE cc_start: 0.9183 (pp) cc_final: 0.8788 (mm) REVERT: B 397 GLN cc_start: 0.8456 (mt0) cc_final: 0.8118 (mm-40) REVERT: B 456 GLU cc_start: 0.8534 (pt0) cc_final: 0.8270 (tt0) REVERT: B 538 GLU cc_start: 0.9027 (tt0) cc_final: 0.8712 (tp30) REVERT: B 556 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 98 THR cc_start: 0.8571 (p) cc_final: 0.8217 (t) REVERT: C 144 THR cc_start: 0.8941 (m) cc_final: 0.8610 (p) REVERT: C 166 TYR cc_start: 0.9069 (m-10) cc_final: 0.8721 (m-10) REVERT: C 176 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6195 (pp20) REVERT: C 262 MET cc_start: 0.8950 (ptm) cc_final: 0.8180 (tpp) REVERT: C 348 GLU cc_start: 0.8945 (tt0) cc_final: 0.8709 (tm-30) REVERT: C 461 GLU cc_start: 0.8704 (tt0) cc_final: 0.8375 (tm-30) REVERT: C 467 ILE cc_start: 0.9310 (pt) cc_final: 0.8805 (mp) REVERT: C 503 VAL cc_start: 0.9180 (p) cc_final: 0.8717 (p) REVERT: C 507 CYS cc_start: 0.8996 (t) cc_final: 0.8690 (t) REVERT: C 516 MET cc_start: 0.9048 (tpt) cc_final: 0.8831 (tpp) REVERT: C 536 ILE cc_start: 0.8214 (tp) cc_final: 0.7865 (tp) REVERT: C 553 TYR cc_start: 0.7788 (m-80) cc_final: 0.7469 (m-80) REVERT: C 558 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8794 (tm-30) REVERT: D 110 LYS cc_start: 0.8537 (mtpt) cc_final: 0.7979 (tptt) REVERT: D 135 ILE cc_start: 0.9460 (mt) cc_final: 0.9038 (mt) REVERT: D 229 ILE cc_start: 0.9470 (mm) cc_final: 0.9104 (mm) REVERT: D 342 GLU cc_start: 0.8929 (tp30) cc_final: 0.8661 (tp30) REVERT: D 345 ARG cc_start: 0.9069 (mtt180) cc_final: 0.8468 (mmm160) REVERT: D 368 LYS cc_start: 0.9083 (pptt) cc_final: 0.8675 (tptt) REVERT: D 382 LEU cc_start: 0.9603 (mp) cc_final: 0.9352 (mm) REVERT: D 409 ARG cc_start: 0.8995 (mtt180) cc_final: 0.8427 (ttm110) REVERT: E 8 TYR cc_start: 0.9142 (m-80) cc_final: 0.8898 (m-80) REVERT: E 232 ILE cc_start: 0.9576 (mm) cc_final: 0.9371 (mt) REVERT: E 249 HIS cc_start: 0.8812 (m-70) cc_final: 0.8448 (m-70) REVERT: E 275 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8608 (tt0) REVERT: E 283 TYR cc_start: 0.8655 (m-80) cc_final: 0.8450 (m-80) REVERT: E 362 MET cc_start: 0.9344 (ttp) cc_final: 0.9130 (ttp) REVERT: E 376 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8647 (tptm) REVERT: E 429 ASN cc_start: 0.8756 (t0) cc_final: 0.8483 (m-40) REVERT: E 437 GLN cc_start: 0.8629 (tt0) cc_final: 0.7804 (tm-30) REVERT: F 26 ASP cc_start: 0.8857 (t70) cc_final: 0.8572 (t0) REVERT: F 37 ASP cc_start: 0.8741 (t0) cc_final: 0.8512 (t70) REVERT: F 49 GLU cc_start: 0.9162 (tt0) cc_final: 0.8718 (tm-30) REVERT: F 54 TYR cc_start: 0.8867 (p90) cc_final: 0.8545 (p90) REVERT: F 79 VAL cc_start: 0.8895 (m) cc_final: 0.8678 (p) REVERT: F 223 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7447 (tptp) REVERT: F 232 ILE cc_start: 0.9646 (mm) cc_final: 0.9426 (tp) REVERT: F 372 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6927 (ttm170) REVERT: F 425 GLN cc_start: 0.8315 (pt0) cc_final: 0.8064 (pt0) REVERT: G 8 ARG cc_start: 0.8495 (tpp-160) cc_final: 0.7989 (tpp-160) REVERT: G 128 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.7829 (tmm160) REVERT: G 131 ARG cc_start: 0.6716 (ttt180) cc_final: 0.6107 (mtp180) REVERT: G 173 ARG cc_start: 0.9098 (mmm-85) cc_final: 0.8720 (ttm-80) REVERT: G 180 GLN cc_start: 0.8762 (mt0) cc_final: 0.8540 (mt0) REVERT: G 187 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8500 (tm-30) REVERT: H 13 PHE cc_start: 0.8493 (m-80) cc_final: 0.8149 (m-80) REVERT: H 19 GLU cc_start: 0.6373 (tt0) cc_final: 0.5389 (mp0) REVERT: I 41 LYS cc_start: 0.7058 (ptpp) cc_final: 0.6485 (pttm) REVERT: I 93 GLU cc_start: 0.8830 (tt0) cc_final: 0.8405 (tm-30) REVERT: J 58 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7899 (ttp80) REVERT: J 100 TRP cc_start: 0.4117 (p-90) cc_final: 0.3714 (t60) REVERT: J 105 ARG cc_start: 0.9272 (ppt-90) cc_final: 0.8865 (ttp80) REVERT: J 112 LEU cc_start: 0.8384 (mp) cc_final: 0.8101 (tt) REVERT: J 170 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7641 (mmm160) REVERT: K 49 LYS cc_start: 0.6266 (pttm) cc_final: 0.5869 (mmtm) REVERT: K 95 GLU cc_start: 0.8436 (tp30) cc_final: 0.7869 (tt0) REVERT: L 45 ARG cc_start: 0.3283 (ppt90) cc_final: 0.3007 (ttp-110) REVERT: L 109 LEU cc_start: 0.8844 (tt) cc_final: 0.8460 (tp) REVERT: L 141 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7921 (tm-30) REVERT: L 165 ASN cc_start: 0.7916 (t0) cc_final: 0.7639 (t0) REVERT: L 175 TRP cc_start: 0.7722 (t-100) cc_final: 0.7320 (t-100) outliers start: 10 outliers final: 6 residues processed: 1049 average time/residue: 0.3003 time to fit residues: 473.2257 Evaluate side-chains 662 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 656 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 218 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 50.0000 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 202 ASN A 260 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 477 GLN B 3 GLN B 459 GLN B 496 GLN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN D 170 GLN D 428 GLN D 458 HIS E 198 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 252 HIS F 413 GLN ** F 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 185 GLN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115057 restraints weight = 69808.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112435 restraints weight = 41794.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113313 restraints weight = 37320.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114163 restraints weight = 29064.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114524 restraints weight = 24172.124| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 40710 Z= 0.262 Angle : 0.761 11.141 55346 Z= 0.394 Chirality : 0.047 0.329 6416 Planarity : 0.006 0.069 7460 Dihedral : 6.486 98.171 6281 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.27 % Allowed : 12.06 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.07 (0.10), residues: 5793 helix: -0.14 (0.09), residues: 3156 sheet: -2.62 (0.20), residues: 540 loop : -2.93 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 532 TYR 0.022 0.002 TYR K 73 PHE 0.020 0.002 PHE A 269 TRP 0.028 0.002 TRP C 438 HIS 0.009 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00601 (40710) covalent geometry : angle 0.76068 (55346) hydrogen bonds : bond 0.04362 ( 2671) hydrogen bonds : angle 4.86289 ( 7863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 715 time to evaluate : 1.464 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASP cc_start: 0.8200 (p0) cc_final: 0.7967 (p0) REVERT: A 281 LEU cc_start: 0.9310 (tp) cc_final: 0.9107 (tt) REVERT: A 291 THR cc_start: 0.9153 (m) cc_final: 0.8868 (p) REVERT: A 336 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 347 GLU cc_start: 0.7690 (pt0) cc_final: 0.7419 (pm20) REVERT: A 348 GLU cc_start: 0.6940 (tt0) cc_final: 0.6584 (tt0) REVERT: A 361 PHE cc_start: 0.8892 (t80) cc_final: 0.8584 (t80) REVERT: A 567 MET cc_start: 0.8544 (mmm) cc_final: 0.8133 (mmm) REVERT: B 128 GLU cc_start: 0.8394 (tp30) cc_final: 0.7908 (tp30) REVERT: B 220 MET cc_start: 0.8291 (tpt) cc_final: 0.7837 (tpp) REVERT: B 337 ILE cc_start: 0.9242 (pp) cc_final: 0.8753 (mm) REVERT: B 461 GLU cc_start: 0.8411 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 98 THR cc_start: 0.8439 (p) cc_final: 0.8134 (t) REVERT: C 311 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8131 (mt-10) REVERT: C 378 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8285 (t) REVERT: C 467 ILE cc_start: 0.8992 (pt) cc_final: 0.8791 (mp) REVERT: C 536 ILE cc_start: 0.8056 (tp) cc_final: 0.7619 (tp) REVERT: D 229 ILE cc_start: 0.9412 (mm) cc_final: 0.9065 (mm) REVERT: D 268 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8378 (tmm-80) REVERT: D 409 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7659 (ttm110) REVERT: E 8 TYR cc_start: 0.8467 (m-80) cc_final: 0.8185 (m-80) REVERT: E 232 ILE cc_start: 0.9458 (mm) cc_final: 0.9152 (mt) REVERT: E 437 GLN cc_start: 0.7762 (tt0) cc_final: 0.7138 (tm-30) REVERT: E 462 TYR cc_start: 0.7223 (m-80) cc_final: 0.6411 (m-80) REVERT: F 88 MET cc_start: 0.7965 (mtp) cc_final: 0.7714 (mtp) REVERT: F 131 ILE cc_start: 0.8725 (pt) cc_final: 0.8318 (mt) REVERT: F 223 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7717 (tptp) REVERT: F 290 ASP cc_start: 0.8180 (t70) cc_final: 0.7844 (t70) REVERT: G 128 ARG cc_start: 0.9050 (mmm-85) cc_final: 0.8112 (tmm160) REVERT: G 131 ARG cc_start: 0.5952 (ttt180) cc_final: 0.5592 (mtp180) REVERT: H 8 GLU cc_start: 0.7819 (pp20) cc_final: 0.7517 (pm20) REVERT: H 13 PHE cc_start: 0.8122 (m-80) cc_final: 0.7553 (m-80) REVERT: H 19 GLU cc_start: 0.6069 (tt0) cc_final: 0.5211 (mp0) REVERT: H 34 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8893 (tm-30) REVERT: H 49 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: H 92 GLU cc_start: 0.7856 (pp20) cc_final: 0.7470 (pp20) REVERT: H 93 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7245 (mt) REVERT: I 73 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: I 82 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: I 91 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8085 (mmm-85) REVERT: I 93 GLU cc_start: 0.8708 (tt0) cc_final: 0.8396 (tm-30) REVERT: J 109 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8125 (tt) REVERT: J 165 ASN cc_start: 0.8198 (t0) cc_final: 0.7926 (t0) REVERT: J 187 TRP cc_start: 0.7938 (m-90) cc_final: 0.7616 (m-10) REVERT: L 24 GLU cc_start: 0.6645 (mm-30) cc_final: 0.5763 (pp20) REVERT: L 87 VAL cc_start: 0.8483 (m) cc_final: 0.8081 (p) REVERT: L 165 ASN cc_start: 0.7851 (t0) cc_final: 0.7522 (t0) outliers start: 106 outliers final: 57 residues processed: 787 average time/residue: 0.2747 time to fit residues: 337.5018 Evaluate side-chains 688 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 624 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 73 TYR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 86 optimal weight: 0.6980 chunk 358 optimal weight: 40.0000 chunk 31 optimal weight: 0.9980 chunk 481 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 533 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 516 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 316 GLN B 418 HIS B 496 GLN B 571 GLN D 448 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN F 458 HIS G 13 GLN J 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.157917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124778 restraints weight = 68931.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120869 restraints weight = 59227.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122244 restraints weight = 47921.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122146 restraints weight = 28753.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122209 restraints weight = 25842.184| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40710 Z= 0.123 Angle : 0.634 11.539 55346 Z= 0.324 Chirality : 0.043 0.246 6416 Planarity : 0.005 0.070 7460 Dihedral : 5.641 84.762 6279 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.65 % Allowed : 13.92 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.94 (0.11), residues: 5793 helix: 0.92 (0.09), residues: 3170 sheet: -2.32 (0.21), residues: 536 loop : -2.62 (0.12), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 409 TYR 0.030 0.002 TYR H 89 PHE 0.021 0.001 PHE C 574 TRP 0.013 0.001 TRP C 330 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00259 (40710) covalent geometry : angle 0.63431 (55346) hydrogen bonds : bond 0.03624 ( 2671) hydrogen bonds : angle 4.43673 ( 7863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 756 time to evaluate : 1.452 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7967 (t0) cc_final: 0.7314 (t0) REVERT: A 213 ASP cc_start: 0.7836 (p0) cc_final: 0.7526 (p0) REVERT: A 257 GLU cc_start: 0.7065 (tt0) cc_final: 0.6847 (tt0) REVERT: A 336 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7556 (tm-30) REVERT: A 347 GLU cc_start: 0.7601 (pt0) cc_final: 0.7291 (pm20) REVERT: B 81 ASN cc_start: 0.9077 (t0) cc_final: 0.8746 (t0) REVERT: B 98 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 128 GLU cc_start: 0.8053 (tp30) cc_final: 0.7578 (tp30) REVERT: B 213 ASP cc_start: 0.8201 (m-30) cc_final: 0.7987 (t0) REVERT: B 220 MET cc_start: 0.8086 (tpt) cc_final: 0.7800 (tpp) REVERT: B 509 MET cc_start: 0.8403 (mtm) cc_final: 0.7942 (mtm) REVERT: C 24 MET cc_start: 0.8082 (ttt) cc_final: 0.7774 (ttt) REVERT: C 98 THR cc_start: 0.8176 (p) cc_final: 0.7849 (t) REVERT: C 253 VAL cc_start: 0.9257 (t) cc_final: 0.8832 (m) REVERT: C 467 ILE cc_start: 0.9000 (pt) cc_final: 0.8785 (tt) REVERT: C 516 MET cc_start: 0.8253 (tpp) cc_final: 0.7967 (tpp) REVERT: C 523 TYR cc_start: 0.8343 (t80) cc_final: 0.7998 (t80) REVERT: C 536 ILE cc_start: 0.7919 (tp) cc_final: 0.7623 (tp) REVERT: C 540 LEU cc_start: 0.8702 (mt) cc_final: 0.8420 (mt) REVERT: C 567 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7717 (ttm) REVERT: D 229 ILE cc_start: 0.9267 (mm) cc_final: 0.8899 (mm) REVERT: E 232 ILE cc_start: 0.9356 (mm) cc_final: 0.9039 (mt) REVERT: E 251 TYR cc_start: 0.8289 (m-10) cc_final: 0.7942 (m-80) REVERT: E 437 GLN cc_start: 0.7668 (tt0) cc_final: 0.6976 (tm-30) REVERT: E 462 TYR cc_start: 0.7145 (m-80) cc_final: 0.6341 (m-80) REVERT: F 82 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8352 (mt) REVERT: F 131 ILE cc_start: 0.8733 (pt) cc_final: 0.8308 (mt) REVERT: F 254 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9219 (tt) REVERT: F 407 ASN cc_start: 0.7743 (m110) cc_final: 0.7519 (m110) REVERT: G 8 ARG cc_start: 0.6614 (tpp-160) cc_final: 0.6293 (tpp-160) REVERT: G 128 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.7942 (tmm160) REVERT: H 19 GLU cc_start: 0.6146 (tt0) cc_final: 0.5352 (mp0) REVERT: H 93 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7305 (mm) REVERT: I 100 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7887 (mtp85) REVERT: J 74 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: L 24 GLU cc_start: 0.5955 (mm-30) cc_final: 0.5234 (pp20) REVERT: L 87 VAL cc_start: 0.8043 (m) cc_final: 0.7761 (p) outliers start: 86 outliers final: 42 residues processed: 815 average time/residue: 0.2779 time to fit residues: 352.5192 Evaluate side-chains 681 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 633 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 386 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 496 optimal weight: 9.9990 chunk 527 optimal weight: 9.9990 chunk 459 optimal weight: 50.0000 chunk 557 optimal weight: 30.0000 chunk 283 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 238 GLN A 397 GLN B 496 GLN B 571 GLN C 196 GLN C 260 ASN C 501 HIS D 23 ASN D 142 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123835 restraints weight = 68831.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118071 restraints weight = 76527.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119879 restraints weight = 68497.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120326 restraints weight = 39306.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120639 restraints weight = 31856.727| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 40710 Z= 0.210 Angle : 0.671 11.338 55346 Z= 0.342 Chirality : 0.045 0.193 6416 Planarity : 0.005 0.061 7460 Dihedral : 5.461 72.519 6279 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.73 % Allowed : 15.74 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.42 (0.11), residues: 5793 helix: 1.42 (0.09), residues: 3177 sheet: -2.31 (0.20), residues: 573 loop : -2.49 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 15 TYR 0.024 0.002 TYR F 383 PHE 0.015 0.002 PHE C 559 TRP 0.028 0.002 TRP J 187 HIS 0.011 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00489 (40710) covalent geometry : angle 0.67120 (55346) hydrogen bonds : bond 0.03713 ( 2671) hydrogen bonds : angle 4.34927 ( 7863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 645 time to evaluate : 1.530 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.9252 (tp) cc_final: 0.9034 (tp) REVERT: A 336 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 98 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8333 (p) REVERT: B 128 GLU cc_start: 0.8199 (tp30) cc_final: 0.7734 (tp30) REVERT: B 220 MET cc_start: 0.8230 (tpt) cc_final: 0.7751 (tpp) REVERT: C 35 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8862 (mt) REVERT: C 98 THR cc_start: 0.8196 (p) cc_final: 0.7893 (t) REVERT: C 438 TRP cc_start: 0.8829 (t60) cc_final: 0.8411 (t60) REVERT: C 536 ILE cc_start: 0.8093 (tp) cc_final: 0.7783 (tp) REVERT: C 540 LEU cc_start: 0.8703 (mt) cc_final: 0.8405 (mt) REVERT: C 567 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7627 (ttm) REVERT: D 229 ILE cc_start: 0.9371 (mm) cc_final: 0.9011 (mm) REVERT: E 232 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9046 (mt) REVERT: E 251 TYR cc_start: 0.8335 (m-10) cc_final: 0.8093 (m-80) REVERT: E 318 ASP cc_start: 0.6745 (t0) cc_final: 0.6536 (t0) REVERT: E 437 GLN cc_start: 0.7658 (tt0) cc_final: 0.7341 (tm-30) REVERT: E 462 TYR cc_start: 0.7176 (m-80) cc_final: 0.6447 (m-80) REVERT: F 131 ILE cc_start: 0.8832 (pt) cc_final: 0.8458 (mt) REVERT: F 132 GLN cc_start: 0.7776 (tt0) cc_final: 0.7531 (tt0) REVERT: F 254 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9249 (tt) REVERT: F 296 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7422 (mm-30) REVERT: F 407 ASN cc_start: 0.7899 (m110) cc_final: 0.7656 (m110) REVERT: G 128 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8004 (tmm160) REVERT: H 19 GLU cc_start: 0.6216 (tt0) cc_final: 0.5436 (mp0) REVERT: I 46 GLU cc_start: 0.6279 (tp30) cc_final: 0.5237 (pt0) REVERT: I 100 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7894 (mtp85) REVERT: J 105 ARG cc_start: 0.7440 (ptm-80) cc_final: 0.7036 (tmm160) REVERT: J 110 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7565 (tt0) REVERT: L 24 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5395 (pp20) REVERT: L 165 ASN cc_start: 0.7317 (t0) cc_final: 0.7074 (t0) outliers start: 121 outliers final: 78 residues processed: 726 average time/residue: 0.2759 time to fit residues: 313.0737 Evaluate side-chains 691 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 608 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 211 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 282 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 405 optimal weight: 50.0000 chunk 485 optimal weight: 50.0000 chunk 174 optimal weight: 7.9990 chunk 344 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 313 optimal weight: 30.0000 chunk 324 optimal weight: 4.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 571 GLN D 23 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN G 13 GLN J 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122382 restraints weight = 68872.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117677 restraints weight = 61563.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119255 restraints weight = 60585.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119552 restraints weight = 34421.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119745 restraints weight = 29094.239| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 40710 Z= 0.223 Angle : 0.679 10.831 55346 Z= 0.345 Chirality : 0.045 0.291 6416 Planarity : 0.005 0.057 7460 Dihedral : 5.388 71.114 6279 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.20 % Allowed : 16.29 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 5793 helix: 1.71 (0.09), residues: 3177 sheet: -2.29 (0.19), residues: 621 loop : -2.42 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 84 TYR 0.023 0.002 TYR H 89 PHE 0.017 0.002 PHE C 574 TRP 0.019 0.002 TRP J 187 HIS 0.012 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00521 (40710) covalent geometry : angle 0.67926 (55346) hydrogen bonds : bond 0.03718 ( 2671) hydrogen bonds : angle 4.30209 ( 7863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 651 time to evaluate : 1.471 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 98 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 220 MET cc_start: 0.8427 (tpt) cc_final: 0.7982 (tpp) REVERT: B 441 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: C 98 THR cc_start: 0.8191 (p) cc_final: 0.7893 (t) REVERT: C 527 GLU cc_start: 0.7599 (tm-30) cc_final: 0.6915 (tm-30) REVERT: C 536 ILE cc_start: 0.8104 (tp) cc_final: 0.7856 (tp) REVERT: C 567 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7629 (ttm) REVERT: D 229 ILE cc_start: 0.9410 (mm) cc_final: 0.9025 (mm) REVERT: E 232 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9033 (mt) REVERT: E 318 ASP cc_start: 0.6786 (t0) cc_final: 0.6543 (t0) REVERT: E 420 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7922 (ttp-170) REVERT: E 437 GLN cc_start: 0.7781 (tt0) cc_final: 0.7415 (tm-30) REVERT: E 462 TYR cc_start: 0.7129 (m-80) cc_final: 0.6399 (m-80) REVERT: F 82 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8419 (tp) REVERT: F 131 ILE cc_start: 0.8863 (pt) cc_final: 0.8472 (mt) REVERT: F 290 ASP cc_start: 0.8133 (t70) cc_final: 0.7608 (t70) REVERT: F 407 ASN cc_start: 0.7942 (m110) cc_final: 0.7702 (m110) REVERT: G 8 ARG cc_start: 0.6783 (tpp-160) cc_final: 0.6516 (tpp-160) REVERT: G 128 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8071 (tmm160) REVERT: H 19 GLU cc_start: 0.6461 (tt0) cc_final: 0.5567 (mp0) REVERT: H 32 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8111 (mt) REVERT: H 49 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6602 (mm-30) REVERT: I 46 GLU cc_start: 0.6241 (tp30) cc_final: 0.4935 (pt0) REVERT: I 82 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: J 105 ARG cc_start: 0.7394 (ptm-80) cc_final: 0.6981 (tmm160) REVERT: J 110 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7662 (tt0) REVERT: J 187 TRP cc_start: 0.7713 (m-90) cc_final: 0.7458 (m-10) REVERT: L 24 GLU cc_start: 0.6138 (mm-30) cc_final: 0.5314 (pp20) REVERT: L 43 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7129 (mp10) REVERT: L 100 TRP cc_start: 0.7232 (t60) cc_final: 0.6797 (t60) REVERT: L 165 ASN cc_start: 0.7489 (t0) cc_final: 0.7285 (t0) outliers start: 136 outliers final: 93 residues processed: 744 average time/residue: 0.2662 time to fit residues: 313.5380 Evaluate side-chains 706 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 605 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 89 TYR Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 115 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 403 optimal weight: 30.0000 chunk 260 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 399 optimal weight: 50.0000 chunk 526 optimal weight: 10.0000 chunk 478 optimal weight: 50.0000 chunk 173 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 239 GLN B 571 GLN C 196 GLN C 290 ASN D 23 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 82 GLN J 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119591 restraints weight = 69583.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114727 restraints weight = 70094.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116485 restraints weight = 64286.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116626 restraints weight = 37390.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117004 restraints weight = 30783.615| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 40710 Z= 0.277 Angle : 0.725 11.114 55346 Z= 0.368 Chirality : 0.047 0.243 6416 Planarity : 0.005 0.054 7460 Dihedral : 5.486 70.884 6279 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.69 % Allowed : 17.80 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.06 (0.12), residues: 5793 helix: 1.79 (0.09), residues: 3180 sheet: -2.30 (0.20), residues: 607 loop : -2.41 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 84 TYR 0.020 0.002 TYR F 383 PHE 0.020 0.002 PHE C 141 TRP 0.016 0.002 TRP C 407 HIS 0.015 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00650 (40710) covalent geometry : angle 0.72517 (55346) hydrogen bonds : bond 0.03862 ( 2671) hydrogen bonds : angle 4.36995 ( 7863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 614 time to evaluate : 1.410 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash REVERT: A 258 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8223 (mtt-85) REVERT: A 336 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 25 TYR cc_start: 0.8967 (m-80) cc_final: 0.8583 (m-80) REVERT: B 98 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 220 MET cc_start: 0.8464 (tpt) cc_final: 0.8005 (tpp) REVERT: B 255 CYS cc_start: 0.8480 (t) cc_final: 0.7783 (p) REVERT: B 391 MET cc_start: 0.7982 (mpp) cc_final: 0.7480 (mmt) REVERT: B 457 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8442 (tt) REVERT: C 98 THR cc_start: 0.8261 (p) cc_final: 0.7989 (t) REVERT: C 378 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8375 (t) REVERT: C 516 MET cc_start: 0.8303 (tpp) cc_final: 0.7986 (tpp) REVERT: C 536 ILE cc_start: 0.8173 (tp) cc_final: 0.7964 (tp) REVERT: C 567 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7566 (ttm) REVERT: D 144 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8499 (mp) REVERT: E 232 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9049 (mt) REVERT: E 251 TYR cc_start: 0.8197 (m-80) cc_final: 0.7969 (m-80) REVERT: E 318 ASP cc_start: 0.7017 (t0) cc_final: 0.6680 (t0) REVERT: E 420 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7992 (ttp-170) REVERT: E 437 GLN cc_start: 0.7843 (tt0) cc_final: 0.7482 (tm-30) REVERT: F 82 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8509 (tp) REVERT: F 131 ILE cc_start: 0.8906 (pt) cc_final: 0.8445 (mt) REVERT: F 254 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9142 (tt) REVERT: F 290 ASP cc_start: 0.8201 (t70) cc_final: 0.7727 (t70) REVERT: F 433 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6916 (mm-30) REVERT: G 8 ARG cc_start: 0.7076 (tpp-160) cc_final: 0.6620 (tpp-160) REVERT: G 128 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8051 (tmm160) REVERT: H 19 GLU cc_start: 0.6397 (tt0) cc_final: 0.5548 (mp0) REVERT: H 32 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8282 (mm) REVERT: H 49 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6674 (mm-30) REVERT: I 82 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: J 59 ARG cc_start: 0.4435 (tmt170) cc_final: 0.4234 (tmt170) REVERT: J 105 ARG cc_start: 0.7424 (ptm-80) cc_final: 0.6959 (tmm160) REVERT: J 110 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7619 (tt0) REVERT: J 187 TRP cc_start: 0.7817 (m-90) cc_final: 0.7597 (m-10) REVERT: K 111 VAL cc_start: 0.7567 (m) cc_final: 0.7111 (t) REVERT: L 24 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5453 (pp20) REVERT: L 43 GLN cc_start: 0.7746 (tp-100) cc_final: 0.6790 (mp10) REVERT: L 100 TRP cc_start: 0.7299 (t60) cc_final: 0.6416 (t60) outliers start: 152 outliers final: 108 residues processed: 718 average time/residue: 0.2727 time to fit residues: 308.6010 Evaluate side-chains 707 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 587 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 575 LYS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 277 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 351 optimal weight: 10.0000 chunk 429 optimal weight: 0.9980 chunk 437 optimal weight: 50.0000 chunk 357 optimal weight: 7.9990 chunk 522 optimal weight: 50.0000 chunk 558 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 571 GLN C 196 GLN D 23 ASN D 148 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123006 restraints weight = 68521.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118681 restraints weight = 61997.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119886 restraints weight = 58213.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120156 restraints weight = 35749.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120328 restraints weight = 28956.515| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40710 Z= 0.147 Angle : 0.637 11.748 55346 Z= 0.322 Chirality : 0.044 0.225 6416 Planarity : 0.004 0.051 7460 Dihedral : 5.153 68.875 6279 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.73 % Allowed : 19.19 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 5793 helix: 2.00 (0.09), residues: 3168 sheet: -2.08 (0.20), residues: 564 loop : -2.24 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 409 TYR 0.020 0.001 TYR F 383 PHE 0.018 0.001 PHE C 574 TRP 0.012 0.001 TRP J 187 HIS 0.010 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00332 (40710) covalent geometry : angle 0.63738 (55346) hydrogen bonds : bond 0.03463 ( 2671) hydrogen bonds : angle 4.17914 ( 7863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 639 time to evaluate : 1.458 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8334 (mtm-85) REVERT: A 258 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7832 (mtt-85) REVERT: A 323 MET cc_start: 0.8575 (mpp) cc_final: 0.8336 (mmp) REVERT: A 336 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 25 TYR cc_start: 0.8900 (m-80) cc_final: 0.8527 (m-80) REVERT: B 81 ASN cc_start: 0.9054 (t0) cc_final: 0.8637 (t0) REVERT: B 98 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8437 (p) REVERT: B 128 GLU cc_start: 0.8179 (tp30) cc_final: 0.7901 (tp30) REVERT: B 213 ASP cc_start: 0.8027 (t0) cc_final: 0.7630 (t0) REVERT: B 220 MET cc_start: 0.8358 (tpt) cc_final: 0.7960 (tpp) REVERT: B 255 CYS cc_start: 0.8392 (t) cc_final: 0.7808 (p) REVERT: B 391 MET cc_start: 0.7915 (mpp) cc_final: 0.7336 (mmt) REVERT: B 441 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: C 98 THR cc_start: 0.8226 (p) cc_final: 0.7889 (t) REVERT: C 209 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8331 (ptp) REVERT: C 361 PHE cc_start: 0.9045 (t80) cc_final: 0.8737 (t80) REVERT: C 524 LYS cc_start: 0.8312 (tppt) cc_final: 0.8001 (tppt) REVERT: C 527 GLU cc_start: 0.7652 (tm-30) cc_final: 0.6932 (tm-30) REVERT: C 536 ILE cc_start: 0.8147 (tp) cc_final: 0.7901 (tp) REVERT: C 567 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7524 (ttm) REVERT: D 88 MET cc_start: 0.7585 (mtt) cc_final: 0.7180 (mtt) REVERT: D 144 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8248 (mp) REVERT: D 200 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: D 267 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9096 (tp) REVERT: E 232 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9018 (mt) REVERT: E 318 ASP cc_start: 0.6863 (t0) cc_final: 0.6524 (t0) REVERT: E 420 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7932 (ttp-170) REVERT: E 437 GLN cc_start: 0.7730 (tt0) cc_final: 0.7381 (tm-30) REVERT: E 462 TYR cc_start: 0.7163 (m-80) cc_final: 0.6399 (m-80) REVERT: F 82 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8442 (mt) REVERT: F 131 ILE cc_start: 0.8783 (pt) cc_final: 0.8107 (mt) REVERT: F 254 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9123 (tt) REVERT: F 290 ASP cc_start: 0.8118 (t70) cc_final: 0.7472 (t70) REVERT: G 8 ARG cc_start: 0.6842 (tpp-160) cc_final: 0.6462 (tpp-160) REVERT: G 128 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8020 (tmm160) REVERT: H 19 GLU cc_start: 0.6416 (tt0) cc_final: 0.5540 (mp0) REVERT: H 32 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8103 (mt) REVERT: I 46 GLU cc_start: 0.5978 (tp30) cc_final: 0.5250 (pt0) REVERT: I 82 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: J 105 ARG cc_start: 0.7360 (ptm-80) cc_final: 0.6854 (tmm160) REVERT: J 110 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7672 (tt0) REVERT: L 24 GLU cc_start: 0.6101 (mm-30) cc_final: 0.5291 (pp20) REVERT: L 43 GLN cc_start: 0.7688 (tp-100) cc_final: 0.6750 (mp10) outliers start: 121 outliers final: 80 residues processed: 720 average time/residue: 0.2775 time to fit residues: 313.8392 Evaluate side-chains 690 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 595 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 575 LYS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 506 optimal weight: 50.0000 chunk 561 optimal weight: 8.9990 chunk 288 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 458 optimal weight: 0.0270 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 397 GLN B 459 GLN B 571 GLN C 238 GLN D 23 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN G 13 GLN G 185 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126033 restraints weight = 68618.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122867 restraints weight = 65045.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123918 restraints weight = 51826.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123877 restraints weight = 31759.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123970 restraints weight = 27793.425| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.002 0.043 40710 Z= 0.115 Angle : 0.619 11.947 55346 Z= 0.311 Chirality : 0.043 0.207 6416 Planarity : 0.004 0.049 7460 Dihedral : 4.815 68.294 6279 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.87 % Allowed : 20.46 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.49 (0.12), residues: 5793 helix: 2.18 (0.09), residues: 3167 sheet: -1.95 (0.21), residues: 545 loop : -2.08 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 409 TYR 0.025 0.001 TYR I 73 PHE 0.018 0.001 PHE C 574 TRP 0.029 0.002 TRP L 100 HIS 0.006 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00250 (40710) covalent geometry : angle 0.61906 (55346) hydrogen bonds : bond 0.03181 ( 2671) hydrogen bonds : angle 4.04641 ( 7863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 673 time to evaluate : 1.175 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7975 (t0) cc_final: 0.7262 (t0) REVERT: A 210 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8341 (mtm-85) REVERT: A 258 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7386 (mtt-85) REVERT: A 294 MET cc_start: 0.8256 (mtt) cc_final: 0.7953 (mtt) REVERT: A 336 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 25 TYR cc_start: 0.8769 (m-80) cc_final: 0.8356 (m-80) REVERT: B 81 ASN cc_start: 0.8922 (t0) cc_final: 0.8612 (t0) REVERT: B 98 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 128 GLU cc_start: 0.8047 (tp30) cc_final: 0.7796 (tp30) REVERT: B 213 ASP cc_start: 0.7788 (t0) cc_final: 0.7442 (t0) REVERT: B 220 MET cc_start: 0.8252 (tpt) cc_final: 0.7938 (tpp) REVERT: B 255 CYS cc_start: 0.8194 (t) cc_final: 0.7723 (p) REVERT: C 85 ASP cc_start: 0.8457 (p0) cc_final: 0.8170 (p0) REVERT: C 98 THR cc_start: 0.8182 (p) cc_final: 0.7761 (t) REVERT: C 209 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8150 (ptp) REVERT: C 253 VAL cc_start: 0.9327 (t) cc_final: 0.8895 (m) REVERT: C 516 MET cc_start: 0.8196 (tpp) cc_final: 0.7995 (tpp) REVERT: C 527 GLU cc_start: 0.7663 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 567 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7414 (ttm) REVERT: D 144 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 200 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: D 229 ILE cc_start: 0.8923 (mm) cc_final: 0.8666 (mm) REVERT: D 411 TYR cc_start: 0.8712 (m-10) cc_final: 0.8314 (m-10) REVERT: E 232 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8937 (mt) REVERT: E 346 LYS cc_start: 0.8812 (pttm) cc_final: 0.8457 (ptmm) REVERT: E 353 ASP cc_start: 0.8251 (p0) cc_final: 0.7935 (p0) REVERT: E 462 TYR cc_start: 0.7171 (m-80) cc_final: 0.6488 (m-80) REVERT: F 82 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8373 (mt) REVERT: F 254 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9188 (tt) REVERT: F 290 ASP cc_start: 0.7946 (t70) cc_final: 0.7266 (t0) REVERT: G 8 ARG cc_start: 0.6859 (tpp-160) cc_final: 0.6472 (tpp-160) REVERT: G 128 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8058 (tmm160) REVERT: H 19 GLU cc_start: 0.6456 (tt0) cc_final: 0.5593 (mp0) REVERT: I 46 GLU cc_start: 0.6326 (tp30) cc_final: 0.5151 (pt0) REVERT: I 82 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: J 105 ARG cc_start: 0.7234 (ptm-80) cc_final: 0.6740 (tmm160) REVERT: J 110 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7665 (tt0) REVERT: L 43 GLN cc_start: 0.7628 (tp-100) cc_final: 0.6694 (mp10) outliers start: 93 outliers final: 58 residues processed: 736 average time/residue: 0.2739 time to fit residues: 318.1022 Evaluate side-chains 682 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 613 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 510 optimal weight: 30.0000 chunk 296 optimal weight: 4.9990 chunk 550 optimal weight: 50.0000 chunk 495 optimal weight: 0.9990 chunk 452 optimal weight: 9.9990 chunk 414 optimal weight: 0.0670 chunk 515 optimal weight: 9.9990 chunk 340 optimal weight: 40.0000 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 496 GLN B 571 GLN D 23 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN G 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124720 restraints weight = 68908.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120266 restraints weight = 64388.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121538 restraints weight = 54636.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121741 restraints weight = 34896.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121873 restraints weight = 27583.982| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40710 Z= 0.130 Angle : 0.646 17.463 55346 Z= 0.323 Chirality : 0.043 0.267 6416 Planarity : 0.004 0.055 7460 Dihedral : 4.743 67.600 6279 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.78 % Allowed : 20.80 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.59 (0.12), residues: 5793 helix: 2.21 (0.09), residues: 3182 sheet: -1.83 (0.21), residues: 540 loop : -2.01 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 84 TYR 0.017 0.001 TYR F 383 PHE 0.015 0.001 PHE C 574 TRP 0.032 0.002 TRP J 187 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00297 (40710) covalent geometry : angle 0.64589 (55346) hydrogen bonds : bond 0.03195 ( 2671) hydrogen bonds : angle 3.99878 ( 7863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 630 time to evaluate : 1.600 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8078 (t0) cc_final: 0.7357 (t0) REVERT: A 294 MET cc_start: 0.8274 (mtt) cc_final: 0.7987 (mtt) REVERT: A 336 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 25 TYR cc_start: 0.8803 (m-80) cc_final: 0.8368 (m-80) REVERT: B 81 ASN cc_start: 0.8936 (t0) cc_final: 0.8618 (t0) REVERT: B 98 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 128 GLU cc_start: 0.8182 (tp30) cc_final: 0.7921 (tp30) REVERT: B 213 ASP cc_start: 0.7816 (t0) cc_final: 0.7466 (t0) REVERT: B 220 MET cc_start: 0.8253 (tpt) cc_final: 0.7945 (tpp) REVERT: B 255 CYS cc_start: 0.8167 (t) cc_final: 0.7684 (p) REVERT: C 85 ASP cc_start: 0.8480 (p0) cc_final: 0.8181 (p0) REVERT: C 98 THR cc_start: 0.8171 (p) cc_final: 0.7779 (t) REVERT: C 209 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8038 (ptp) REVERT: C 253 VAL cc_start: 0.9395 (t) cc_final: 0.8959 (m) REVERT: C 438 TRP cc_start: 0.8762 (t60) cc_final: 0.8241 (t60) REVERT: C 516 MET cc_start: 0.8176 (tpp) cc_final: 0.7926 (tpp) REVERT: C 527 GLU cc_start: 0.7557 (tm-30) cc_final: 0.6843 (tm-30) REVERT: C 540 LEU cc_start: 0.8877 (mm) cc_final: 0.8597 (mt) REVERT: C 567 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7485 (ttm) REVERT: D 62 GLU cc_start: 0.6470 (pm20) cc_final: 0.6185 (pm20) REVERT: D 144 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8169 (mp) REVERT: D 411 TYR cc_start: 0.8719 (m-10) cc_final: 0.8289 (m-10) REVERT: E 232 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8954 (mt) REVERT: E 346 LYS cc_start: 0.8763 (pttm) cc_final: 0.8429 (ptmm) REVERT: E 353 ASP cc_start: 0.8369 (p0) cc_final: 0.8033 (p0) REVERT: E 462 TYR cc_start: 0.7263 (m-80) cc_final: 0.6555 (m-80) REVERT: F 82 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8431 (mt) REVERT: F 254 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9100 (tt) REVERT: F 290 ASP cc_start: 0.8038 (t70) cc_final: 0.7382 (t0) REVERT: G 8 ARG cc_start: 0.6860 (tpp-160) cc_final: 0.6479 (tpp-160) REVERT: G 128 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8093 (tmm160) REVERT: H 19 GLU cc_start: 0.6711 (tt0) cc_final: 0.5668 (mp0) REVERT: H 32 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8130 (mt) REVERT: I 46 GLU cc_start: 0.6177 (tp30) cc_final: 0.4964 (pt0) REVERT: I 82 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: J 105 ARG cc_start: 0.7353 (ptm-80) cc_final: 0.6858 (tmm160) REVERT: J 110 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7767 (tt0) REVERT: J 187 TRP cc_start: 0.7451 (m-10) cc_final: 0.7095 (m-10) outliers start: 90 outliers final: 71 residues processed: 688 average time/residue: 0.2782 time to fit residues: 302.7167 Evaluate side-chains 685 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 605 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 245 optimal weight: 2.9990 chunk 394 optimal weight: 50.0000 chunk 387 optimal weight: 10.0000 chunk 505 optimal weight: 50.0000 chunk 313 optimal weight: 20.0000 chunk 329 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 513 optimal weight: 50.0000 chunk 379 optimal weight: 6.9990 chunk 571 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 571 GLN D 23 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN G 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123222 restraints weight = 68806.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.118503 restraints weight = 76175.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120380 restraints weight = 65603.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120333 restraints weight = 37788.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120620 restraints weight = 31178.907| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 40710 Z= 0.190 Angle : 0.694 14.727 55346 Z= 0.349 Chirality : 0.045 0.303 6416 Planarity : 0.005 0.087 7460 Dihedral : 4.843 65.948 6279 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.81 % Allowed : 20.83 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.57 (0.12), residues: 5793 helix: 2.21 (0.09), residues: 3184 sheet: -1.89 (0.21), residues: 576 loop : -2.02 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 420 TYR 0.018 0.002 TYR C 166 PHE 0.013 0.002 PHE C 141 TRP 0.053 0.002 TRP L 100 HIS 0.006 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00447 (40710) covalent geometry : angle 0.69402 (55346) hydrogen bonds : bond 0.03381 ( 2671) hydrogen bonds : angle 4.06816 ( 7863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11586 Ramachandran restraints generated. 5793 Oldfield, 0 Emsley, 5793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 611 time to evaluate : 1.510 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 TARDY: cannot create tardy model for: "PRO J 146 " (corrupted residue). Skipping it. Corrupt residue: chain: J residue: PRO 146 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8253 (t0) cc_final: 0.7266 (t0) REVERT: A 258 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8061 (mtt-85) REVERT: A 323 MET cc_start: 0.8352 (mpp) cc_final: 0.7812 (mmp) REVERT: A 336 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 25 TYR cc_start: 0.8891 (m-80) cc_final: 0.8564 (m-80) REVERT: B 81 ASN cc_start: 0.9013 (t0) cc_final: 0.8618 (t0) REVERT: B 98 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 213 ASP cc_start: 0.7821 (t0) cc_final: 0.7488 (t0) REVERT: B 220 MET cc_start: 0.8299 (tpt) cc_final: 0.7947 (tpp) REVERT: B 255 CYS cc_start: 0.8217 (t) cc_final: 0.7754 (p) REVERT: C 209 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8156 (ptp) REVERT: C 516 MET cc_start: 0.8177 (tpp) cc_final: 0.7927 (tpp) REVERT: C 567 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7460 (ttm) REVERT: D 62 GLU cc_start: 0.6561 (pm20) cc_final: 0.6230 (pm20) REVERT: D 200 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: D 411 TYR cc_start: 0.8718 (m-10) cc_final: 0.8271 (m-10) REVERT: E 232 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9000 (mt) REVERT: E 346 LYS cc_start: 0.8765 (pttm) cc_final: 0.8447 (ptmm) REVERT: E 353 ASP cc_start: 0.8365 (p0) cc_final: 0.8047 (p0) REVERT: E 462 TYR cc_start: 0.7182 (m-80) cc_final: 0.6471 (m-80) REVERT: F 82 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (mt) REVERT: F 254 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9127 (tt) REVERT: F 274 ARG cc_start: 0.7106 (ptt-90) cc_final: 0.6849 (ptp90) REVERT: F 290 ASP cc_start: 0.8204 (t70) cc_final: 0.7591 (t70) REVERT: G 8 ARG cc_start: 0.6860 (tpp-160) cc_final: 0.6500 (tpp-160) REVERT: G 128 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8023 (tmm160) REVERT: H 19 GLU cc_start: 0.6832 (tt0) cc_final: 0.5768 (mp0) REVERT: H 32 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8016 (mt) REVERT: I 42 LYS cc_start: 0.5841 (mptt) cc_final: 0.5536 (ptmm) REVERT: I 46 GLU cc_start: 0.6135 (tp30) cc_final: 0.4998 (pt0) REVERT: I 116 LYS cc_start: 0.8069 (mptt) cc_final: 0.7820 (mmtm) REVERT: J 105 ARG cc_start: 0.7281 (ptm-80) cc_final: 0.6801 (tmm160) REVERT: J 110 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7737 (tt0) REVERT: J 187 TRP cc_start: 0.7473 (m-10) cc_final: 0.7100 (m-10) outliers start: 91 outliers final: 74 residues processed: 673 average time/residue: 0.2745 time to fit residues: 290.1035 Evaluate side-chains 679 residues out of total 4578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 596 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 567 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 264 CYS Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 24 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 353 optimal weight: 10.0000 chunk 295 optimal weight: 0.9990 chunk 535 optimal weight: 10.0000 chunk 382 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 464 optimal weight: 40.0000 chunk 277 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN C 260 ASN D 23 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.157351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124292 restraints weight = 69114.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120256 restraints weight = 72708.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121475 restraints weight = 70603.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121784 restraints weight = 41502.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121944 restraints weight = 33453.585| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40710 Z= 0.161 Angle : 0.676 14.088 55346 Z= 0.339 Chirality : 0.044 0.303 6416 Planarity : 0.004 0.092 7460 Dihedral : 4.807 63.979 6279 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.02 % Allowed : 21.07 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.64 (0.12), residues: 5793 helix: 2.23 (0.09), residues: 3188 sheet: -1.80 (0.21), residues: 573 loop : -1.95 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 420 TYR 0.026 0.001 TYR C 166 PHE 0.013 0.001 PHE C 48 TRP 0.042 0.002 TRP L 100 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00376 (40710) covalent geometry : angle 0.67623 (55346) hydrogen bonds : bond 0.03293 ( 2671) hydrogen bonds : angle 4.04876 ( 7863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7371.82 seconds wall clock time: 127 minutes 46.58 seconds (7666.58 seconds total)