Starting phenix.real_space_refine on Wed May 6 12:46:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2r_65577/05_2026/9w2r_65577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2r_65577/05_2026/9w2r_65577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w2r_65577/05_2026/9w2r_65577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2r_65577/05_2026/9w2r_65577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w2r_65577/05_2026/9w2r_65577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2r_65577/05_2026/9w2r_65577.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 14 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 24895 2.51 5 N 6667 2.21 5 O 7358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 241 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39088 Number of models: 1 Model: "" Number of chains: 34 Chain: "8" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 298 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3870 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 17, 'TRANS': 490} Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3710 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 17, 'TRANS': 468} Chain: "C" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3834 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "D" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3558 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 23, 'TRANS': 445} Chain: "E" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3539 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain: "F" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3539 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain: "G" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2115 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 970 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 369 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 525 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 528 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 528 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 538 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1447 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "a" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 213} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1619 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "d" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1224 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 142} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "e" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 207 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "f" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "g" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 570 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 73} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "h" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 514 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "j" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 352 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "k" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 261 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.79, per 1000 atoms: 0.25 Number of scatterers: 39088 At special positions: 0 Unit cell: (152.6, 174.4, 239.8, 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 149 16.00 P 14 15.00 Mg 5 11.99 O 7358 8.00 N 6667 7.00 C 24895 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9382 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 26 sheets defined 60.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain '8' and resid 1 through 13 removed outlier: 3.924A pdb=" N ASP 8 5 " --> pdb=" O PRO 8 2 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR 8 6 " --> pdb=" O GLN 8 3 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER 8 7 " --> pdb=" O LEU 8 4 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR 8 8 " --> pdb=" O ASP 8 5 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR 8 11 " --> pdb=" O THR 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 14 through 21 removed outlier: 3.638A pdb=" N LEU 8 18 " --> pdb=" O LEU 8 14 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 30 removed outlier: 3.633A pdb=" N LYS 8 30 " --> pdb=" O LEU 8 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 removed outlier: 4.380A pdb=" N GLU A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.583A pdb=" N VAL A 23 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.509A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.958A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.745A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.834A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.726A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.546A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.543A pdb=" N ILE A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.203A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.590A pdb=" N GLN A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.607A pdb=" N PHE A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.259A pdb=" N LYS A 455 " --> pdb=" O TYR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 507 Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.078A pdb=" N LEU B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.877A pdb=" N ILE B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 224 through 227 removed outlier: 4.100A pdb=" N LYS B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 3.661A pdb=" N TYR B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.853A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.748A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.890A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.748A pdb=" N ALA B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.792A pdb=" N ILE C 11 " --> pdb=" O GLU C 7 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 12 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.745A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.873A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 4.100A pdb=" N ILE C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 3.966A pdb=" N TYR C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.722A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.557A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.504A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 removed outlier: 3.666A pdb=" N ASN C 341 " --> pdb=" O TYR C 337 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 342 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 removed outlier: 3.612A pdb=" N GLY C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 removed outlier: 4.117A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 437 through 451 removed outlier: 3.606A pdb=" N ALA C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 455 removed outlier: 3.902A pdb=" N LYS C 455 " --> pdb=" O TYR C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 452 through 455' Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 476 removed outlier: 3.571A pdb=" N SER C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 161 through 174 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 225 through 248 removed outlier: 3.521A pdb=" N ARG D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 270 removed outlier: 3.980A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.703A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 326 Processing helix chain 'D' and resid 336 through 343 removed outlier: 3.887A pdb=" N LEU D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.501A pdb=" N GLY D 364 " --> pdb=" O PRO D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.935A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 391 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 477 removed outlier: 3.827A pdb=" N ALA D 466 " --> pdb=" O PRO D 462 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 231 through 247 removed outlier: 3.602A pdb=" N TYR E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE E 243 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 247 " --> pdb=" O PHE E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 273 removed outlier: 3.958A pdb=" N PHE E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.734A pdb=" N MET E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 364 through 392 removed outlier: 4.017A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 425 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 453 through 458 removed outlier: 4.360A pdb=" N PHE E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 453 through 458' Processing helix chain 'E' and resid 462 through 474 removed outlier: 3.561A pdb=" N ALA E 466 " --> pdb=" O PRO E 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 471 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 161 through 174 removed outlier: 3.699A pdb=" N LEU F 165 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 225 through 247 removed outlier: 5.137A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 4.015A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 326 removed outlier: 3.875A pdb=" N THR F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE F 326 " --> pdb=" O PRO F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 383 removed outlier: 3.571A pdb=" N TYR F 368 " --> pdb=" O GLY F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 392 Processing helix chain 'F' and resid 397 through 414 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 453 through 458 removed outlier: 3.606A pdb=" N PHE F 457 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR F 458 " --> pdb=" O GLN F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 475 removed outlier: 3.570A pdb=" N ALA F 466 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 475 " --> pdb=" O ASP F 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 55 removed outlier: 4.057A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.659A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 109 through 116 Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.789A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 removed outlier: 3.956A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 272 removed outlier: 3.541A pdb=" N ASP G 233 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'H' and resid 124 through 145 Processing helix chain 'I' and resid 2 through 7 removed outlier: 3.886A pdb=" N GLN I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA I 7 " --> pdb=" O TYR I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 7' Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 27 through 36 removed outlier: 3.782A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 20 through 52 removed outlier: 3.527A pdb=" N TYR J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 14 through 16 No H-bonds generated for 'chain 'K' and resid 14 through 16' Processing helix chain 'K' and resid 17 through 39 removed outlier: 4.283A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 62 removed outlier: 3.643A pdb=" N LEU K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 73 Processing helix chain 'L' and resid 2 through 14 Processing helix chain 'L' and resid 15 through 39 Processing helix chain 'L' and resid 42 through 73 removed outlier: 3.605A pdb=" N LEU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE L 73 " --> pdb=" O PHE L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 12 removed outlier: 3.744A pdb=" N ALA M 6 " --> pdb=" O ILE M 2 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 15 No H-bonds generated for 'chain 'M' and resid 13 through 15' Processing helix chain 'M' and resid 16 through 39 removed outlier: 3.536A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 72 removed outlier: 5.660A pdb=" N VAL M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA M 68 " --> pdb=" O CYS M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 removed outlier: 4.136A pdb=" N ILE N 9 " --> pdb=" O ALA N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 39 removed outlier: 4.337A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 73 removed outlier: 4.097A pdb=" N ALA N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA N 68 " --> pdb=" O CYS N 64 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 removed outlier: 3.773A pdb=" N PHE O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 39 removed outlier: 4.059A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 73 removed outlier: 4.245A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 removed outlier: 3.616A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 39 removed outlier: 4.144A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 73 removed outlier: 4.049A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 39 removed outlier: 4.289A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE Q 9 " --> pdb=" O ALA Q 5 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA Q 14 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 74 removed outlier: 3.980A pdb=" N VAL Q 67 " --> pdb=" O PHE Q 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 removed outlier: 3.593A pdb=" N LYS R 7 " --> pdb=" O ASP R 3 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 17 No H-bonds generated for 'chain 'R' and resid 15 through 17' Processing helix chain 'R' and resid 18 through 39 removed outlier: 4.149A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 74 removed outlier: 3.895A pdb=" N ALA R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 28 removed outlier: 4.078A pdb=" N LYS S 28 " --> pdb=" O SER S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 46 Processing helix chain 'S' and resid 48 through 57 removed outlier: 3.601A pdb=" N SER S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'S' and resid 79 through 93 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 127 through 139 removed outlier: 3.608A pdb=" N LYS S 139 " --> pdb=" O LYS S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 188 removed outlier: 3.902A pdb=" N LYS S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 7 Processing helix chain 'a' and resid 19 through 31 removed outlier: 3.538A pdb=" N ILE a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 40 through 59 removed outlier: 3.894A pdb=" N LYS a 55 " --> pdb=" O GLN a 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN a 56 " --> pdb=" O LEU a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 67 Processing helix chain 'a' and resid 68 through 87 removed outlier: 3.699A pdb=" N LEU a 77 " --> pdb=" O MET a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 97 removed outlier: 3.663A pdb=" N THR a 96 " --> pdb=" O THR a 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN a 97 " --> pdb=" O PRO a 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 93 through 97' Processing helix chain 'a' and resid 98 through 104 Processing helix chain 'a' and resid 105 through 121 removed outlier: 3.505A pdb=" N TRP a 109 " --> pdb=" O ALA a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 122 through 124 No H-bonds generated for 'chain 'a' and resid 122 through 124' Processing helix chain 'a' and resid 137 through 180 removed outlier: 4.108A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE a 147 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER a 148 " --> pdb=" O ILE a 144 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 4.198A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU a 169 " --> pdb=" O THR a 165 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 190 Processing helix chain 'a' and resid 192 through 224 removed outlier: 4.022A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR a 212 " --> pdb=" O MET a 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 32 through 49 removed outlier: 4.692A pdb=" N ILE b 42 " --> pdb=" O GLY b 38 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU b 49 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 119 removed outlier: 4.142A pdb=" N ALA b 60 " --> pdb=" O GLU b 56 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS b 89 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA b 91 " --> pdb=" O GLU b 87 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN b 92 " --> pdb=" O GLN b 88 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU b 93 " --> pdb=" O LYS b 89 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU b 94 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA b 116 " --> pdb=" O LYS b 112 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU b 117 " --> pdb=" O SER b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 156 removed outlier: 3.906A pdb=" N ASP b 126 " --> pdb=" O HIS b 122 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN b 128 " --> pdb=" O LEU b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 156 through 185 removed outlier: 3.780A pdb=" N SER b 160 " --> pdb=" O ASP b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 209 removed outlier: 3.834A pdb=" N ALA b 195 " --> pdb=" O LYS b 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS b 196 " --> pdb=" O GLU b 192 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN b 209 " --> pdb=" O SER b 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 16 removed outlier: 4.360A pdb=" N GLY d 16 " --> pdb=" O TRP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 44 removed outlier: 3.943A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL d 26 " --> pdb=" O ASN d 22 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN d 28 " --> pdb=" O LYS d 24 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 57 Processing helix chain 'd' and resid 62 through 76 Processing helix chain 'd' and resid 90 through 101 removed outlier: 3.654A pdb=" N LYS d 94 " --> pdb=" O ASP d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 123 removed outlier: 3.568A pdb=" N GLU d 119 " --> pdb=" O GLU d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 139 removed outlier: 3.837A pdb=" N GLU d 137 " --> pdb=" O GLU d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 143 Processing helix chain 'e' and resid 7 through 33 removed outlier: 3.713A pdb=" N LEU e 20 " --> pdb=" O SER e 16 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA e 23 " --> pdb=" O PHE e 19 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA e 26 " --> pdb=" O MET e 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 17 No H-bonds generated for 'chain 'f' and resid 15 through 17' Processing helix chain 'f' and resid 18 through 26 removed outlier: 3.597A pdb=" N LEU f 24 " --> pdb=" O PRO f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 49 removed outlier: 4.085A pdb=" N GLN f 38 " --> pdb=" O ALA f 34 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR f 41 " --> pdb=" O PHE f 37 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR f 44 " --> pdb=" O GLY f 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS f 47 " --> pdb=" O ARG f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 78 removed outlier: 3.636A pdb=" N MET f 61 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL f 62 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU f 63 " --> pdb=" O LEU f 59 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG f 73 " --> pdb=" O LEU f 69 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS f 76 " --> pdb=" O CYS f 72 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU f 77 " --> pdb=" O ARG f 73 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 81 No H-bonds generated for 'chain 'f' and resid 79 through 81' Processing helix chain 'g' and resid 22 through 37 removed outlier: 3.941A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 44 Processing helix chain 'g' and resid 45 through 62 removed outlier: 4.031A pdb=" N ILE g 49 " --> pdb=" O ILE g 45 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN g 50 " --> pdb=" O PRO g 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU g 52 " --> pdb=" O ALA g 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS g 53 " --> pdb=" O ILE g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 84 removed outlier: 4.575A pdb=" N VAL g 78 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU g 81 " --> pdb=" O LEU g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 94 removed outlier: 3.607A pdb=" N ILE g 91 " --> pdb=" O TYR g 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY g 93 " --> pdb=" O GLY g 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 25 Processing helix chain 'h' and resid 31 through 51 removed outlier: 4.153A pdb=" N TYR h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 18 removed outlier: 4.664A pdb=" N ILE j 11 " --> pdb=" O LYS j 7 " (cutoff:3.500A) Proline residue: j 12 - end of helix Proline residue: j 15 - end of helix removed outlier: 3.995A pdb=" N THR j 18 " --> pdb=" O LYS j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 49 Processing helix chain 'k' and resid 22 through 37 removed outlier: 3.551A pdb=" N ASN k 28 " --> pdb=" O THR k 24 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR k 34 " --> pdb=" O VAL k 30 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY k 35 " --> pdb=" O LEU k 31 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE k 37 " --> pdb=" O THR k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 47 removed outlier: 4.135A pdb=" N LEU k 42 " --> pdb=" O ALA k 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.815A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 29 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.948A pdb=" N ALA A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.463A pdb=" N ILE A 167 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.204A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG F 59 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N HIS F 52 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR F 57 " --> pdb=" O HIS F 52 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL F 16 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP F 22 " --> pdb=" O VAL F 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.763A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.612A pdb=" N ASP B 269 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 206 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 167 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.747A pdb=" N ARG D 59 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS D 52 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR D 57 " --> pdb=" O HIS D 52 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D 15 " --> pdb=" O ASP D 22 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN D 24 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILE D 13 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 63 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 91 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 90 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU C 27 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL S 116 " --> pdb=" O LYS S 149 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU S 151 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS S 118 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.747A pdb=" N ARG D 59 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS D 52 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR D 57 " --> pdb=" O HIS D 52 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D 15 " --> pdb=" O ASP D 22 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN D 24 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ILE D 13 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL S 116 " --> pdb=" O LYS S 149 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU S 151 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS S 118 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.136A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.952A pdb=" N ILE C 206 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.934A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.238A pdb=" N GLN D 112 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 94 through 95 removed outlier: 6.480A pdb=" N MET D 95 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 256 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 186 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE D 152 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE D 310 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 154 " --> pdb=" O ILE D 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.273A pdb=" N TYR D 146 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 17 removed outlier: 6.882A pdb=" N ASP E 22 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL E 16 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 21 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR E 57 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N HIS E 52 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG E 59 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 86 removed outlier: 4.032A pdb=" N VAL E 86 " --> pdb=" O GLN E 112 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN E 112 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 94 through 95 removed outlier: 6.217A pdb=" N MET E 95 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLN E 221 " --> pdb=" O MET E 95 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 182 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE E 152 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 331 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 132 through 133 removed outlier: 4.212A pdb=" N TYR E 146 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 83 through 86 removed outlier: 3.563A pdb=" N VAL F 86 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN F 112 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.190A pdb=" N MET F 95 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR F 180 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE F 152 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE F 310 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU F 154 " --> pdb=" O ILE F 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 132 through 133 removed outlier: 4.209A pdb=" N TYR F 146 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 171 through 179 removed outlier: 6.626A pdb=" N LEU G 67 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE G 69 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ASN G 163 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N VAL G 71 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N PHE G 165 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU G 125 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR G 127 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY G 107 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS G 129 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 26 through 31 removed outlier: 5.316A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 45 through 47 removed outlier: 4.322A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 12 through 13 2259 hydrogen bonds defined for protein. 6546 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: 8.86 Time building geometry restraints manager: 4.72 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: 11378 1.33 - 1.46: 6069 1.46 - 1.58: 21965 1.58 - 1.70: 19 1.70 - 1.82: 277 Bond restraints: 39708 Sorted by residual: bond pdb=" C5' ATP C 601 " pdb=" O5' ATP C 601 " ideal model delta sigma weight residual 1.443 1.336 0.107 1.00e-02 1.00e+04 1.15e+02 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " ideal model delta sigma weight residual 1.426 1.518 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C5 ADP F 501 " pdb=" C6 ADP F 501 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.346 0.042 1.00e-02 1.00e+04 1.73e+01 ... (remaining 39703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 53422 3.94 - 7.89: 268 7.89 - 11.83: 32 11.83 - 15.77: 8 15.77 - 19.71: 3 Bond angle restraints: 53733 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.96 15.91 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 124.54 15.33 1.00e+00 1.00e+00 2.35e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.26 13.57 1.00e+00 1.00e+00 1.84e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 129.94 9.93 1.00e+00 1.00e+00 9.86e+01 angle pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " pdb=" O3G ATP A 601 " ideal model delta sigma weight residual 104.48 115.74 -11.26 1.14e+00 7.76e-01 9.85e+01 ... (remaining 53728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.45: 21888 20.45 - 40.90: 1779 40.90 - 61.34: 338 61.34 - 81.79: 61 81.79 - 102.24: 25 Dihedral angle restraints: 24091 sinusoidal: 9444 harmonic: 14647 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 42.24 -102.24 1 2.00e+01 2.50e-03 2.91e+01 dihedral pdb=" CA PHE 8 33 " pdb=" C PHE 8 33 " pdb=" N TYR 8 34 " pdb=" CA TYR 8 34 " ideal model delta harmonic sigma weight residual 180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU a 160 " pdb=" C LEU a 160 " pdb=" N THR a 161 " pdb=" CA THR a 161 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 24088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 6239 0.157 - 0.315: 29 0.315 - 0.472: 2 0.472 - 0.629: 0 0.629 - 0.786: 1 Chirality restraints: 6271 Sorted by residual: chirality pdb=" CG LEU C 410 " pdb=" CB LEU C 410 " pdb=" CD1 LEU C 410 " pdb=" CD2 LEU C 410 " both_signs ideal model delta sigma weight residual False -2.59 -1.80 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA ASP A 270 " pdb=" N ASP A 270 " pdb=" C ASP A 270 " pdb=" CB ASP A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ARG A 362 " pdb=" N ARG A 362 " pdb=" C ARG A 362 " pdb=" CB ARG A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 6268 not shown) Planarity restraints: 6863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 358 " 0.091 2.00e-02 2.50e+03 5.16e-02 5.32e+01 pdb=" CG TYR A 358 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 358 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 358 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 358 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 358 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 358 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 358 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 368 " 0.074 2.00e-02 2.50e+03 3.80e-02 2.89e+01 pdb=" CG TYR D 368 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 368 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR D 368 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR D 368 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 368 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 368 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 368 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE d 125 " 0.050 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO d 126 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO d 126 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO d 126 " 0.042 5.00e-02 4.00e+02 ... (remaining 6860 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 21 2.20 - 2.88: 14174 2.88 - 3.55: 57816 3.55 - 4.23: 81877 4.23 - 4.90: 147417 Nonbonded interactions: 301305 Sorted by model distance: nonbonded pdb=" CE MET N 66 " pdb=" CB ALA a 162 " model vdw 1.529 3.880 nonbonded pdb=" CG ARG B 362 " pdb=" N1 ATP B 601 " model vdw 1.599 2.816 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.759 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 1.767 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.787 2.170 ... (remaining 301300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 508 or resid 601 through 602)) selection = chain 'B' selection = (chain 'C' and resid 23 through 602) } ncs_group { reference = (chain 'D' and resid 9 through 475) selection = chain 'E' selection = (chain 'F' and resid 9 through 475) } ncs_group { reference = (chain 'K' and (resid 1 through 37 or (resid 38 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 or (resid 41 through 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 74)) selection = (chain 'L' and (resid 1 through 37 or (resid 38 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 or (resid 41 through 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 74)) selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and (resid 1 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 74)) selection = (chain 'O' and (resid 1 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 74)) selection = (chain 'P' and (resid 1 through 37 or (resid 38 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 74)) selection = (chain 'Q' and (resid 1 through 37 or (resid 38 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 through 74)) selection = (chain 'R' and (resid 1 through 37 or (resid 38 through 39 and (name N or name C \ A or name C or name O or name CB )) or resid 40 or (resid 41 through 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 74)) } 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 individual isotropic 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: 9.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 37.960 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 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 : 0.007 0.655 39714 Z= 0.632 Angle : 0.757 19.715 53733 Z= 0.429 Chirality : 0.047 0.786 6271 Planarity : 0.004 0.077 6863 Dihedral : 15.498 102.239 14709 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 0.27 % Allowed : 15.43 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 5053 helix: 1.59 (0.10), residues: 2654 sheet: 0.65 (0.23), residues: 537 loop : -0.55 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 59 TYR 0.091 0.002 TYR A 358 PHE 0.046 0.001 PHE 8 21 TRP 0.021 0.001 TRP a 68 HIS 0.006 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00395 (39708) covalent geometry : angle 0.75682 (53733) hydrogen bonds : bond 0.13215 ( 2233) hydrogen bonds : angle 5.70178 ( 6546) Misc. bond : bond 0.48118 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 759 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8085 (m-30) cc_final: 0.7865 (m-30) REVERT: A 70 ASN cc_start: 0.8213 (p0) cc_final: 0.7935 (p0) REVERT: A 333 ASP cc_start: 0.7822 (t0) cc_final: 0.7613 (t0) REVERT: A 393 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7234 (tp30) REVERT: A 477 GLN cc_start: 0.6188 (mm-40) cc_final: 0.5547 (tm-30) REVERT: B 171 ARG cc_start: 0.7256 (mtm-85) cc_final: 0.6873 (mtm110) REVERT: B 191 ASP cc_start: 0.7529 (m-30) cc_final: 0.7242 (p0) REVERT: B 226 MET cc_start: 0.7645 (tpt) cc_final: 0.7443 (tpp) REVERT: B 281 MET cc_start: 0.6942 (mmm) cc_final: 0.6317 (mtp) REVERT: B 355 GLU cc_start: 0.7427 (tp30) cc_final: 0.7102 (tm-30) REVERT: B 359 LYS cc_start: 0.7308 (ttmm) cc_final: 0.6959 (ttpt) REVERT: B 488 LYS cc_start: 0.8273 (ptmt) cc_final: 0.7605 (ttmm) REVERT: C 32 LEU cc_start: 0.7759 (mt) cc_final: 0.7074 (mp) REVERT: C 62 MET cc_start: 0.7617 (ttm) cc_final: 0.7022 (ttp) REVERT: C 86 ASP cc_start: 0.8220 (t0) cc_final: 0.7936 (t0) REVERT: C 143 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7632 (mtt-85) REVERT: C 477 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7187 (tm-30) REVERT: C 498 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8142 (ttmm) REVERT: D 55 GLU cc_start: 0.8786 (pt0) cc_final: 0.8586 (pm20) REVERT: D 61 ILE cc_start: 0.8086 (pt) cc_final: 0.7876 (mt) REVERT: D 76 LEU cc_start: 0.7707 (tp) cc_final: 0.7130 (mm) REVERT: D 294 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8058 (mt-10) REVERT: D 393 MET cc_start: 0.7266 (mmm) cc_final: 0.6736 (mmm) REVERT: D 448 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 207 ASN cc_start: 0.8125 (t0) cc_final: 0.7352 (t0) REVERT: E 289 MET cc_start: 0.6838 (tpp) cc_final: 0.6365 (tpp) REVERT: E 292 MET cc_start: 0.8570 (ttp) cc_final: 0.7814 (tmm) REVERT: E 352 ASP cc_start: 0.8090 (m-30) cc_final: 0.7711 (m-30) REVERT: E 354 THR cc_start: 0.8384 (m) cc_final: 0.8106 (p) REVERT: F 67 GLU cc_start: 0.7835 (pm20) cc_final: 0.7445 (pm20) REVERT: G 57 ILE cc_start: 0.8006 (mm) cc_final: 0.7713 (tt) REVERT: G 92 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7203 (tm-30) REVERT: G 140 ASP cc_start: 0.8109 (m-30) cc_final: 0.7892 (m-30) REVERT: G 171 TYR cc_start: 0.8191 (p90) cc_final: 0.7491 (p90) REVERT: G 175 GLU cc_start: 0.8076 (tt0) cc_final: 0.7841 (tm-30) REVERT: G 261 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6973 (mt-10) REVERT: G 264 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7481 (mm-30) REVERT: H 35 GLN cc_start: 0.7988 (pm20) cc_final: 0.7541 (pm20) REVERT: H 42 THR cc_start: 0.7457 (t) cc_final: 0.6518 (t) REVERT: H 91 GLN cc_start: 0.6283 (mp10) cc_final: 0.5920 (mp10) REVERT: H 96 GLU cc_start: 0.7717 (tp30) cc_final: 0.7239 (tp30) REVERT: H 113 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8203 (tm-30) REVERT: H 125 GLU cc_start: 0.8317 (mp0) cc_final: 0.8031 (pp20) REVERT: H 141 LEU cc_start: 0.6567 (tp) cc_final: 0.6274 (tp) REVERT: I 23 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7843 (mmm-85) REVERT: I 35 MET cc_start: 0.8559 (mmt) cc_final: 0.8337 (mmt) REVERT: I 43 LYS cc_start: 0.7612 (mmtm) cc_final: 0.7357 (mmtm) REVERT: J 17 ASP cc_start: 0.8267 (t0) cc_final: 0.7941 (t0) REVERT: J 37 ARG cc_start: 0.5778 (mmp80) cc_final: 0.5196 (mtp180) REVERT: N 75 MET cc_start: 0.3246 (tmm) cc_final: 0.3020 (tmm) REVERT: O 60 MET cc_start: 0.3471 (ttt) cc_final: 0.1550 (mmt) REVERT: P 66 MET cc_start: 0.5152 (tmm) cc_final: 0.4554 (mmm) REVERT: Q 60 MET cc_start: 0.3981 (ptm) cc_final: 0.2729 (mmp) REVERT: S 12 TYR cc_start: 0.7937 (m-80) cc_final: 0.7552 (m-80) REVERT: S 155 ASP cc_start: 0.7009 (t0) cc_final: 0.6798 (t70) REVERT: a 1 MET cc_start: 0.2798 (ttt) cc_final: -0.0913 (pmm) REVERT: a 43 VAL cc_start: 0.7297 (t) cc_final: 0.6901 (t) REVERT: a 104 MET cc_start: 0.2898 (mpp) cc_final: 0.1585 (mmm) REVERT: a 202 LEU cc_start: 0.4731 (mt) cc_final: 0.3940 (pp) REVERT: b 124 LEU cc_start: 0.7927 (pt) cc_final: 0.7350 (pt) REVERT: b 125 PHE cc_start: 0.2935 (m-80) cc_final: 0.2138 (p90) REVERT: b 129 ARG cc_start: 0.5713 (mmt-90) cc_final: 0.5226 (mtm180) REVERT: b 154 ARG cc_start: 0.6317 (mmm160) cc_final: 0.6075 (ttm-80) REVERT: b 163 ASN cc_start: 0.8305 (m-40) cc_final: 0.8054 (m-40) REVERT: b 165 MET cc_start: 0.8355 (ptp) cc_final: 0.7528 (mmm) REVERT: b 166 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7591 (mtp180) REVERT: d 51 ILE cc_start: 0.4817 (mp) cc_final: 0.4510 (mt) REVERT: h 36 GLN cc_start: 0.7960 (tp40) cc_final: 0.7584 (tp40) REVERT: h 40 ASP cc_start: 0.8664 (m-30) cc_final: 0.8351 (m-30) REVERT: h 47 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8096 (mttp) REVERT: h 50 TYR cc_start: 0.4184 (m-80) cc_final: 0.3899 (m-10) REVERT: h 58 PHE cc_start: 0.5127 (m-10) cc_final: 0.4623 (m-10) REVERT: j 13 MET cc_start: 0.6834 (tpt) cc_final: 0.5875 (tmm) outliers start: 11 outliers final: 4 residues processed: 768 average time/residue: 0.2380 time to fit residues: 295.5735 Evaluate side-chains 500 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 496 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 345 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN D 249 GLN F 361 ASN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN a 172 HIS a 223 HIS a 225 ASN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 175 ASN d 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.186191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140549 restraints weight = 52761.798| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.59 r_work: 0.3422 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39714 Z= 0.160 Angle : 0.627 14.498 53733 Z= 0.314 Chirality : 0.044 0.308 6271 Planarity : 0.004 0.047 6863 Dihedral : 7.309 117.508 5700 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.23 % Allowed : 16.77 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 5053 helix: 1.68 (0.10), residues: 2641 sheet: 0.57 (0.22), residues: 551 loop : -0.69 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 337 TYR 0.072 0.002 TYR D 345 PHE 0.049 0.002 PHE Q 29 TRP 0.026 0.002 TRP d 53 HIS 0.010 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00366 (39708) covalent geometry : angle 0.62653 (53733) hydrogen bonds : bond 0.04691 ( 2233) hydrogen bonds : angle 4.61995 ( 6546) Misc. bond : bond 0.00326 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 511 time to evaluate : 1.449 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: A 224 ASP cc_start: 0.8580 (t0) cc_final: 0.8159 (t0) REVERT: A 355 GLU cc_start: 0.8557 (tp30) cc_final: 0.8038 (tt0) REVERT: A 393 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7475 (tp30) REVERT: B 210 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7185 (ttp-170) REVERT: B 226 MET cc_start: 0.8712 (tpt) cc_final: 0.8448 (tpp) REVERT: B 488 LYS cc_start: 0.9143 (ptmt) cc_final: 0.8626 (ttmm) REVERT: C 24 ASP cc_start: 0.8285 (t0) cc_final: 0.7273 (t0) REVERT: C 26 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: C 32 LEU cc_start: 0.8520 (mt) cc_final: 0.8170 (mp) REVERT: C 62 MET cc_start: 0.7535 (ttm) cc_final: 0.7128 (ttp) REVERT: C 477 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7902 (tp40) REVERT: D 200 MET cc_start: 0.8218 (tpp) cc_final: 0.7945 (tpp) REVERT: E 207 ASN cc_start: 0.8201 (t0) cc_final: 0.7864 (t0) REVERT: E 354 THR cc_start: 0.9092 (m) cc_final: 0.8678 (p) REVERT: E 393 MET cc_start: 0.6148 (tmm) cc_final: 0.5697 (tmm) REVERT: E 428 LEU cc_start: 0.8652 (tt) cc_final: 0.8308 (mm) REVERT: F 95 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8194 (ttm) REVERT: G 15 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8696 (m-40) REVERT: G 140 ASP cc_start: 0.8386 (m-30) cc_final: 0.7807 (m-30) REVERT: H 34 ARG cc_start: 0.5273 (mmp-170) cc_final: 0.5049 (mmm160) REVERT: H 125 GLU cc_start: 0.8338 (mp0) cc_final: 0.7950 (pp20) REVERT: I 24 ASP cc_start: 0.8316 (p0) cc_final: 0.8115 (p0) REVERT: I 42 ILE cc_start: 0.8973 (mt) cc_final: 0.8321 (mt) REVERT: I 43 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7747 (mmtm) REVERT: J 17 ASP cc_start: 0.8879 (t0) cc_final: 0.8568 (t0) REVERT: J 37 ARG cc_start: 0.7320 (mmp80) cc_final: 0.6663 (mtp180) REVERT: L 65 LEU cc_start: 0.5693 (OUTLIER) cc_final: 0.5435 (mm) REVERT: N 75 MET cc_start: 0.3627 (tmm) cc_final: 0.3415 (tmm) REVERT: O 60 MET cc_start: 0.3938 (ttt) cc_final: 0.1738 (mmp) REVERT: O 75 MET cc_start: 0.1431 (mtp) cc_final: 0.0290 (mmm) REVERT: P 49 TYR cc_start: 0.4011 (OUTLIER) cc_final: 0.3670 (m-10) REVERT: P 66 MET cc_start: 0.5822 (tmm) cc_final: 0.4970 (mmm) REVERT: Q 60 MET cc_start: 0.2665 (ptm) cc_final: 0.1892 (mmp) REVERT: S 180 GLN cc_start: 0.8483 (mp10) cc_final: 0.8259 (mp10) REVERT: a 1 MET cc_start: 0.0936 (ttt) cc_final: -0.2419 (mpp) REVERT: a 43 VAL cc_start: 0.6969 (t) cc_final: 0.6548 (t) REVERT: a 52 LEU cc_start: 0.7528 (tp) cc_final: 0.6911 (mt) REVERT: a 104 MET cc_start: 0.2543 (mpp) cc_final: 0.0865 (tpp) REVERT: a 202 LEU cc_start: 0.5419 (mt) cc_final: 0.4901 (pp) REVERT: b 7 GLU cc_start: 0.6989 (tm-30) cc_final: 0.5742 (tp30) REVERT: b 125 PHE cc_start: 0.3831 (m-80) cc_final: 0.2617 (p90) REVERT: b 129 ARG cc_start: 0.6073 (mmt-90) cc_final: 0.5357 (mtm180) REVERT: b 165 MET cc_start: 0.8428 (ptp) cc_final: 0.7783 (mmm) REVERT: b 166 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7145 (ttp-110) REVERT: d 112 GLN cc_start: 0.5104 (OUTLIER) cc_final: 0.4882 (pt0) REVERT: h 36 GLN cc_start: 0.7894 (tp40) cc_final: 0.7253 (tp40) REVERT: h 40 ASP cc_start: 0.8432 (m-30) cc_final: 0.8006 (m-30) REVERT: h 47 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8666 (mttp) outliers start: 131 outliers final: 76 residues processed: 609 average time/residue: 0.2320 time to fit residues: 234.2970 Evaluate side-chains 528 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 445 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 11 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 31 PHE Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain h residue 7 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 341 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 489 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 219 optimal weight: 0.4980 chunk 304 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 316 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN a 172 HIS a 223 HIS a 225 ASN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 158 HIS d 28 ASN d 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.187965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129282 restraints weight = 57821.166| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.01 r_work: 0.3577 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39714 Z= 0.144 Angle : 0.579 14.521 53733 Z= 0.293 Chirality : 0.043 0.287 6271 Planarity : 0.004 0.050 6863 Dihedral : 7.296 110.262 5700 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.53 % Allowed : 17.43 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 5053 helix: 1.78 (0.10), residues: 2630 sheet: 0.40 (0.22), residues: 560 loop : -0.76 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 337 TYR 0.055 0.001 TYR D 345 PHE 0.025 0.001 PHE E 424 TRP 0.040 0.002 TRP d 53 HIS 0.010 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00335 (39708) covalent geometry : angle 0.57913 (53733) hydrogen bonds : bond 0.04506 ( 2233) hydrogen bonds : angle 4.44441 ( 6546) Misc. bond : bond 0.00365 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 475 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASP cc_start: 0.8784 (t0) cc_final: 0.8340 (t0) REVERT: B 229 THR cc_start: 0.9006 (t) cc_final: 0.8579 (p) REVERT: B 488 LYS cc_start: 0.9130 (ptmt) cc_final: 0.8529 (ttmm) REVERT: C 24 ASP cc_start: 0.8414 (t0) cc_final: 0.7280 (t0) REVERT: C 26 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: C 62 MET cc_start: 0.7884 (ttm) cc_final: 0.7514 (ttp) REVERT: C 445 ILE cc_start: 0.8148 (mm) cc_final: 0.7913 (mt) REVERT: C 477 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7756 (tp40) REVERT: C 496 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8808 (mtmm) REVERT: D 200 MET cc_start: 0.8059 (tpp) cc_final: 0.7715 (tpp) REVERT: D 448 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: E 354 THR cc_start: 0.9040 (m) cc_final: 0.8762 (p) REVERT: E 428 LEU cc_start: 0.8603 (tt) cc_final: 0.8302 (mm) REVERT: F 95 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8315 (ttm) REVERT: G 15 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8599 (m-40) REVERT: G 57 ILE cc_start: 0.8206 (mp) cc_final: 0.7976 (tt) REVERT: G 140 ASP cc_start: 0.8511 (m-30) cc_final: 0.7998 (m-30) REVERT: H 125 GLU cc_start: 0.8468 (mp0) cc_final: 0.8008 (pp20) REVERT: H 132 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7222 (pp30) REVERT: I 35 MET cc_start: 0.8523 (mmt) cc_final: 0.8277 (mmt) REVERT: I 42 ILE cc_start: 0.8843 (mt) cc_final: 0.8335 (mt) REVERT: I 43 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7717 (mmtm) REVERT: J 17 ASP cc_start: 0.9007 (t0) cc_final: 0.8695 (t0) REVERT: J 33 TYR cc_start: 0.7921 (t80) cc_final: 0.7624 (t80) REVERT: J 37 ARG cc_start: 0.7090 (mmp80) cc_final: 0.6610 (mpt180) REVERT: L 47 PHE cc_start: 0.6985 (t80) cc_final: 0.6771 (t80) REVERT: O 47 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5193 (t80) REVERT: O 60 MET cc_start: 0.3862 (ttt) cc_final: 0.1652 (mmp) REVERT: O 75 MET cc_start: 0.0783 (mtp) cc_final: -0.0330 (mmm) REVERT: P 49 TYR cc_start: 0.3979 (OUTLIER) cc_final: 0.3659 (m-10) REVERT: P 66 MET cc_start: 0.5923 (tmm) cc_final: 0.5125 (mmm) REVERT: Q 60 MET cc_start: 0.2750 (ptm) cc_final: 0.1870 (mmp) REVERT: S 44 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8467 (tp-100) REVERT: S 180 GLN cc_start: 0.8401 (mp10) cc_final: 0.8145 (mp10) REVERT: a 1 MET cc_start: 0.1392 (ttt) cc_final: -0.2189 (mpp) REVERT: a 52 LEU cc_start: 0.7348 (tp) cc_final: 0.6805 (mt) REVERT: a 104 MET cc_start: 0.2832 (mpp) cc_final: 0.1343 (tpp) REVERT: a 202 LEU cc_start: 0.5252 (mt) cc_final: 0.4722 (pp) REVERT: b 11 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.4163 (tptt) REVERT: b 125 PHE cc_start: 0.4086 (m-80) cc_final: 0.2865 (p90) REVERT: b 129 ARG cc_start: 0.5718 (mmt-90) cc_final: 0.5011 (mtp180) REVERT: b 156 ASP cc_start: 0.7802 (m-30) cc_final: 0.7532 (m-30) REVERT: b 165 MET cc_start: 0.8526 (ptp) cc_final: 0.7897 (mmm) REVERT: b 166 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7393 (tmt170) REVERT: h 36 GLN cc_start: 0.7901 (tp40) cc_final: 0.7382 (tp40) REVERT: h 40 ASP cc_start: 0.8629 (m-30) cc_final: 0.8226 (m-30) REVERT: h 44 PHE cc_start: 0.8644 (t80) cc_final: 0.8347 (t80) REVERT: h 47 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8511 (mttp) REVERT: j 17 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6460 (m-80) outliers start: 143 outliers final: 90 residues processed: 578 average time/residue: 0.2232 time to fit residues: 213.6927 Evaluate side-chains 540 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 441 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 203 LEU Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain j residue 17 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 52 optimal weight: 0.9990 chunk 231 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 152 optimal weight: 0.6980 chunk 495 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 358 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 425 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 3 GLN A 432 GLN C 78 ASN D 442 GLN H 15 GLN H 32 ASN P 44 GLN a 172 HIS a 223 HIS a 225 ASN b 86 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.184229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121552 restraints weight = 52292.442| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.22 r_work: 0.3283 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 39714 Z= 0.115 Angle : 0.549 14.838 53733 Z= 0.276 Chirality : 0.042 0.252 6271 Planarity : 0.004 0.046 6863 Dihedral : 7.049 104.113 5700 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.23 % Allowed : 18.30 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 5053 helix: 1.87 (0.10), residues: 2626 sheet: 0.53 (0.22), residues: 554 loop : -0.70 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 337 TYR 0.043 0.001 TYR D 345 PHE 0.029 0.001 PHE E 424 TRP 0.025 0.001 TRP d 53 HIS 0.007 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00246 (39708) covalent geometry : angle 0.54865 (53733) hydrogen bonds : bond 0.04071 ( 2233) hydrogen bonds : angle 4.28329 ( 6546) Misc. bond : bond 0.00268 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 476 time to evaluate : 1.552 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: A 393 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7850 (mt-10) REVERT: B 210 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6733 (ttp-170) REVERT: B 229 THR cc_start: 0.9165 (t) cc_final: 0.8603 (p) REVERT: B 488 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8329 (ttmm) REVERT: C 24 ASP cc_start: 0.8357 (t0) cc_final: 0.7331 (t0) REVERT: C 26 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: C 62 MET cc_start: 0.7580 (ttm) cc_final: 0.7214 (ttp) REVERT: C 477 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7304 (tm-30) REVERT: C 496 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8755 (mtmm) REVERT: C 497 LEU cc_start: 0.8151 (tp) cc_final: 0.7746 (tp) REVERT: D 52 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.7430 (m90) REVERT: D 200 MET cc_start: 0.7778 (tpp) cc_final: 0.7426 (tpp) REVERT: D 201 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8009 (tt) REVERT: E 207 ASN cc_start: 0.8463 (t0) cc_final: 0.7921 (t0) REVERT: E 337 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8451 (ttm110) REVERT: E 354 THR cc_start: 0.8829 (m) cc_final: 0.8534 (p) REVERT: E 393 MET cc_start: 0.7562 (tpp) cc_final: 0.7355 (mmm) REVERT: E 428 LEU cc_start: 0.8545 (tt) cc_final: 0.8252 (mm) REVERT: F 95 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8305 (ttm) REVERT: G 15 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: G 140 ASP cc_start: 0.8372 (m-30) cc_final: 0.7837 (m-30) REVERT: H 125 GLU cc_start: 0.8437 (mp0) cc_final: 0.7942 (pp20) REVERT: I 35 MET cc_start: 0.8325 (mmt) cc_final: 0.7959 (mmt) REVERT: I 42 ILE cc_start: 0.8595 (mt) cc_final: 0.8110 (mt) REVERT: I 43 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7429 (mmtm) REVERT: J 17 ASP cc_start: 0.8733 (t0) cc_final: 0.8415 (t0) REVERT: L 47 PHE cc_start: 0.6932 (t80) cc_final: 0.6567 (t80) REVERT: O 47 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5179 (t80) REVERT: O 60 MET cc_start: 0.3710 (ttt) cc_final: 0.1564 (mmp) REVERT: P 49 TYR cc_start: 0.3934 (OUTLIER) cc_final: 0.3691 (m-10) REVERT: P 66 MET cc_start: 0.6014 (tmm) cc_final: 0.5260 (mmm) REVERT: Q 60 MET cc_start: 0.2691 (ptm) cc_final: 0.1890 (mmp) REVERT: S 44 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8534 (tp-100) REVERT: S 180 GLN cc_start: 0.8210 (mp10) cc_final: 0.7577 (mp10) REVERT: a 1 MET cc_start: 0.1966 (ttt) cc_final: -0.1102 (mpp) REVERT: a 5 LEU cc_start: 0.4348 (OUTLIER) cc_final: 0.3575 (mp) REVERT: a 73 MET cc_start: 0.3687 (mmm) cc_final: 0.3424 (mmm) REVERT: a 104 MET cc_start: 0.3160 (mpp) cc_final: 0.1249 (tpp) REVERT: a 202 LEU cc_start: 0.5186 (mt) cc_final: 0.4703 (pp) REVERT: b 11 LYS cc_start: 0.5518 (OUTLIER) cc_final: 0.4213 (tptt) REVERT: b 124 LEU cc_start: 0.7782 (pt) cc_final: 0.7536 (pt) REVERT: b 125 PHE cc_start: 0.3473 (m-80) cc_final: 0.2501 (p90) REVERT: b 129 ARG cc_start: 0.5565 (mmt-90) cc_final: 0.4833 (mtm180) REVERT: b 156 ASP cc_start: 0.7602 (m-30) cc_final: 0.7303 (m-30) REVERT: b 165 MET cc_start: 0.8413 (ptp) cc_final: 0.7894 (mmm) REVERT: b 166 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7228 (tmt170) REVERT: h 22 ARG cc_start: 0.6595 (ttp80) cc_final: 0.6371 (ptm160) REVERT: h 36 GLN cc_start: 0.7894 (tp40) cc_final: 0.7350 (tp40) REVERT: h 40 ASP cc_start: 0.8623 (m-30) cc_final: 0.8199 (m-30) REVERT: h 44 PHE cc_start: 0.8571 (t80) cc_final: 0.8335 (t80) REVERT: h 47 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8554 (mttp) REVERT: j 17 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6531 (m-80) outliers start: 131 outliers final: 82 residues processed: 573 average time/residue: 0.2327 time to fit residues: 219.2132 Evaluate side-chains 538 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 444 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 3 GLN Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain j residue 17 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 474 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 394 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 261 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 487 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 chunk 334 optimal weight: 0.7980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN H 15 GLN K 44 GLN a 172 HIS a 223 HIS a 225 ASN b 86 ASN b 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.185193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.139168 restraints weight = 52877.537| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.66 r_work: 0.3457 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 39714 Z= 0.113 Angle : 0.545 14.627 53733 Z= 0.273 Chirality : 0.042 0.248 6271 Planarity : 0.004 0.081 6863 Dihedral : 6.873 98.052 5700 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.36 % Allowed : 18.69 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.12), residues: 5053 helix: 1.93 (0.10), residues: 2623 sheet: 0.51 (0.22), residues: 560 loop : -0.68 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 38 TYR 0.040 0.001 TYR D 345 PHE 0.025 0.001 PHE E 424 TRP 0.026 0.001 TRP d 53 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00246 (39708) covalent geometry : angle 0.54513 (53733) hydrogen bonds : bond 0.03950 ( 2233) hydrogen bonds : angle 4.21874 ( 6546) Misc. bond : bond 0.00237 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 459 time to evaluate : 1.436 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: A 224 ASP cc_start: 0.8595 (t0) cc_final: 0.8152 (t0) REVERT: B 210 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7139 (ttp-170) REVERT: B 229 THR cc_start: 0.8842 (t) cc_final: 0.8493 (p) REVERT: B 281 MET cc_start: 0.7917 (mtm) cc_final: 0.7633 (mtt) REVERT: B 488 LYS cc_start: 0.9117 (ptmt) cc_final: 0.8638 (ttmm) REVERT: C 62 MET cc_start: 0.7423 (ttm) cc_final: 0.7104 (ttp) REVERT: C 140 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8394 (mm) REVERT: C 477 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7545 (tm-30) REVERT: C 496 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8610 (mtmm) REVERT: C 497 LEU cc_start: 0.8439 (tp) cc_final: 0.8108 (tp) REVERT: D 52 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.7497 (m90) REVERT: D 200 MET cc_start: 0.8196 (tpp) cc_final: 0.7899 (tpp) REVERT: D 201 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8589 (tt) REVERT: E 207 ASN cc_start: 0.8414 (t0) cc_final: 0.8091 (t0) REVERT: E 354 THR cc_start: 0.9082 (m) cc_final: 0.8819 (p) REVERT: E 428 LEU cc_start: 0.8566 (tt) cc_final: 0.8324 (mm) REVERT: F 289 MET cc_start: 0.7936 (ttm) cc_final: 0.7608 (mtt) REVERT: F 292 MET cc_start: 0.8744 (tmm) cc_final: 0.8528 (tmm) REVERT: G 15 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: G 140 ASP cc_start: 0.8385 (m-30) cc_final: 0.7747 (m-30) REVERT: H 69 ASP cc_start: 0.6756 (p0) cc_final: 0.6496 (p0) REVERT: H 125 GLU cc_start: 0.8377 (mp0) cc_final: 0.7920 (pp20) REVERT: I 42 ILE cc_start: 0.9041 (mt) cc_final: 0.8550 (mt) REVERT: I 43 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7511 (mmtm) REVERT: J 17 ASP cc_start: 0.8890 (t0) cc_final: 0.8557 (t0) REVERT: J 46 LYS cc_start: 0.8560 (tptm) cc_final: 0.8142 (tptt) REVERT: L 54 PHE cc_start: 0.6841 (t80) cc_final: 0.6400 (t80) REVERT: O 47 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5021 (t80) REVERT: O 60 MET cc_start: 0.4011 (ttt) cc_final: 0.1640 (mmp) REVERT: P 49 TYR cc_start: 0.3989 (OUTLIER) cc_final: 0.3776 (m-10) REVERT: Q 60 MET cc_start: 0.2441 (ptm) cc_final: 0.1828 (mmp) REVERT: S 44 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8482 (tp-100) REVERT: S 180 GLN cc_start: 0.8537 (mp10) cc_final: 0.8289 (mp10) REVERT: a 1 MET cc_start: 0.1113 (ttt) cc_final: -0.1410 (pmm) REVERT: a 5 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.3460 (mp) REVERT: a 31 PHE cc_start: 0.3929 (t80) cc_final: 0.3626 (t80) REVERT: a 52 LEU cc_start: 0.7470 (tp) cc_final: 0.6804 (mt) REVERT: a 53 VAL cc_start: 0.8783 (m) cc_final: 0.8532 (p) REVERT: a 73 MET cc_start: 0.4331 (mmm) cc_final: 0.4018 (mmm) REVERT: a 104 MET cc_start: 0.2909 (mpp) cc_final: 0.1091 (tpp) REVERT: a 202 LEU cc_start: 0.5325 (mt) cc_final: 0.4975 (pp) REVERT: b 125 PHE cc_start: 0.3903 (m-80) cc_final: 0.2569 (p90) REVERT: b 129 ARG cc_start: 0.5634 (mmt-90) cc_final: 0.4888 (mtp180) REVERT: b 156 ASP cc_start: 0.7623 (m-30) cc_final: 0.7333 (m-30) REVERT: b 165 MET cc_start: 0.8332 (ptp) cc_final: 0.7855 (mmm) REVERT: b 166 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7063 (ttp-110) REVERT: h 18 TYR cc_start: 0.6719 (t80) cc_final: 0.5957 (t80) REVERT: h 36 GLN cc_start: 0.7925 (tp40) cc_final: 0.7299 (tp40) REVERT: h 40 ASP cc_start: 0.8409 (m-30) cc_final: 0.7926 (m-30) REVERT: h 44 PHE cc_start: 0.8633 (t80) cc_final: 0.8366 (t80) REVERT: h 47 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8580 (mttp) REVERT: j 17 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6588 (m-80) outliers start: 136 outliers final: 91 residues processed: 561 average time/residue: 0.2214 time to fit residues: 205.8212 Evaluate side-chains 537 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 436 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 203 LEU Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 17 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 489 optimal weight: 0.9980 chunk 119 optimal weight: 0.4980 chunk 355 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 31 HIS C 78 ASN D 51 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN a 172 HIS a 223 HIS b 86 ASN f 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.182994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135516 restraints weight = 53149.377| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.48 r_work: 0.3399 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39714 Z= 0.152 Angle : 0.574 14.346 53733 Z= 0.291 Chirality : 0.043 0.246 6271 Planarity : 0.004 0.073 6863 Dihedral : 6.864 95.334 5698 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.75 % Allowed : 19.19 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 5053 helix: 1.85 (0.10), residues: 2621 sheet: 0.43 (0.22), residues: 554 loop : -0.82 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 337 TYR 0.041 0.001 TYR D 345 PHE 0.031 0.001 PHE E 424 TRP 0.027 0.002 TRP d 53 HIS 0.009 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00360 (39708) covalent geometry : angle 0.57421 (53733) hydrogen bonds : bond 0.04384 ( 2233) hydrogen bonds : angle 4.28339 ( 6546) Misc. bond : bond 0.00263 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 452 time to evaluate : 1.502 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: A 173 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 224 ASP cc_start: 0.8630 (t0) cc_final: 0.8271 (t0) REVERT: B 27 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 210 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7047 (ttp-170) REVERT: B 488 LYS cc_start: 0.9115 (ptmt) cc_final: 0.8540 (ttmm) REVERT: B 499 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: C 62 MET cc_start: 0.7678 (ttm) cc_final: 0.7357 (ttp) REVERT: C 477 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7497 (tm-30) REVERT: C 496 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8666 (mtmm) REVERT: C 497 LEU cc_start: 0.8413 (tp) cc_final: 0.8066 (tp) REVERT: D 52 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.7574 (m90) REVERT: D 200 MET cc_start: 0.8312 (tpp) cc_final: 0.8030 (tpp) REVERT: E 354 THR cc_start: 0.9001 (m) cc_final: 0.8702 (p) REVERT: E 428 LEU cc_start: 0.8606 (tt) cc_final: 0.8358 (mm) REVERT: F 95 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8320 (ttm) REVERT: F 292 MET cc_start: 0.8818 (tmm) cc_final: 0.8532 (tmm) REVERT: G 15 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8641 (m-40) REVERT: G 140 ASP cc_start: 0.8352 (m-30) cc_final: 0.7858 (m-30) REVERT: H 69 ASP cc_start: 0.6722 (p0) cc_final: 0.6435 (p0) REVERT: H 125 GLU cc_start: 0.8386 (mp0) cc_final: 0.8140 (pp20) REVERT: I 24 ASP cc_start: 0.8353 (p0) cc_final: 0.8124 (p0) REVERT: I 35 MET cc_start: 0.7960 (mmt) cc_final: 0.7503 (mmt) REVERT: I 36 LYS cc_start: 0.8464 (mppt) cc_final: 0.7907 (mppt) REVERT: I 42 ILE cc_start: 0.8962 (mt) cc_final: 0.8446 (mt) REVERT: I 43 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7531 (mmtm) REVERT: J 17 ASP cc_start: 0.8857 (t0) cc_final: 0.8525 (t0) REVERT: J 46 LYS cc_start: 0.8571 (tptm) cc_final: 0.8165 (tptt) REVERT: L 54 PHE cc_start: 0.6843 (t80) cc_final: 0.6361 (t80) REVERT: O 47 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5067 (t80) REVERT: O 60 MET cc_start: 0.4069 (ttt) cc_final: 0.1622 (mmp) REVERT: P 49 TYR cc_start: 0.3792 (OUTLIER) cc_final: 0.3579 (m-10) REVERT: Q 60 MET cc_start: 0.2440 (ptm) cc_final: 0.1841 (mmp) REVERT: S 44 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8533 (tp-100) REVERT: S 109 MET cc_start: 0.8521 (mmm) cc_final: 0.8175 (mmm) REVERT: S 151 GLU cc_start: 0.7558 (mp0) cc_final: 0.7254 (mp0) REVERT: S 180 GLN cc_start: 0.8534 (mp10) cc_final: 0.8286 (mp10) REVERT: a 1 MET cc_start: 0.1361 (ttt) cc_final: -0.1269 (pmm) REVERT: a 5 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.3254 (mp) REVERT: a 43 VAL cc_start: 0.6636 (t) cc_final: 0.6340 (p) REVERT: a 53 VAL cc_start: 0.8757 (m) cc_final: 0.8554 (p) REVERT: a 73 MET cc_start: 0.4120 (mmm) cc_final: 0.3828 (mmm) REVERT: a 104 MET cc_start: 0.2963 (mpp) cc_final: 0.2391 (ptt) REVERT: b 7 GLU cc_start: 0.6984 (tm-30) cc_final: 0.5852 (tp30) REVERT: b 11 LYS cc_start: 0.5445 (OUTLIER) cc_final: 0.4161 (tptt) REVERT: b 125 PHE cc_start: 0.4263 (m-80) cc_final: 0.2832 (p90) REVERT: b 129 ARG cc_start: 0.5627 (mmt-90) cc_final: 0.4860 (mtm180) REVERT: b 156 ASP cc_start: 0.7727 (m-30) cc_final: 0.7388 (m-30) REVERT: b 165 MET cc_start: 0.8366 (ptp) cc_final: 0.7860 (mmm) REVERT: b 166 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7068 (ttp-110) REVERT: g 70 LYS cc_start: -0.0458 (OUTLIER) cc_final: -0.1585 (mttt) REVERT: h 36 GLN cc_start: 0.7913 (tp40) cc_final: 0.7290 (tp40) REVERT: h 40 ASP cc_start: 0.8477 (m-30) cc_final: 0.7985 (m-30) REVERT: h 47 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8645 (mttp) REVERT: j 17 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6443 (m-80) outliers start: 152 outliers final: 113 residues processed: 568 average time/residue: 0.2423 time to fit residues: 227.0414 Evaluate side-chains 563 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 436 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 18 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 140 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain b residue 203 LEU Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 17 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 236 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 493 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 339 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN D 51 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS a 223 HIS b 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.183468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135037 restraints weight = 53064.893| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.42 r_work: 0.3419 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39714 Z= 0.135 Angle : 0.565 14.139 53733 Z= 0.285 Chirality : 0.042 0.241 6271 Planarity : 0.004 0.057 6863 Dihedral : 6.795 90.469 5698 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.73 % Allowed : 19.51 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.12), residues: 5053 helix: 1.83 (0.10), residues: 2633 sheet: 0.42 (0.22), residues: 561 loop : -0.86 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 337 TYR 0.047 0.001 TYR D 345 PHE 0.039 0.001 PHE 8 24 TRP 0.027 0.001 TRP d 53 HIS 0.007 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00313 (39708) covalent geometry : angle 0.56468 (53733) hydrogen bonds : bond 0.04244 ( 2233) hydrogen bonds : angle 4.23261 ( 6546) Misc. bond : bond 0.00243 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 449 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: A 17 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 173 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 224 ASP cc_start: 0.8598 (t0) cc_final: 0.8255 (t0) REVERT: B 27 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 210 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7016 (ttp-170) REVERT: B 399 GLU cc_start: 0.8598 (tp30) cc_final: 0.8313 (mt-10) REVERT: B 488 LYS cc_start: 0.9028 (ptmt) cc_final: 0.8521 (ttmm) REVERT: B 499 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: C 62 MET cc_start: 0.7513 (ttm) cc_final: 0.7240 (ttp) REVERT: C 245 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8012 (tp) REVERT: C 477 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7484 (tm-30) REVERT: C 496 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: C 497 LEU cc_start: 0.8419 (tp) cc_final: 0.8078 (tp) REVERT: D 52 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.7491 (m90) REVERT: D 200 MET cc_start: 0.8306 (tpp) cc_final: 0.8001 (tpp) REVERT: E 428 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8347 (mm) REVERT: F 95 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8269 (ttm) REVERT: F 292 MET cc_start: 0.8651 (tmm) cc_final: 0.8330 (tmm) REVERT: G 15 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8642 (m-40) REVERT: G 140 ASP cc_start: 0.8345 (m-30) cc_final: 0.7852 (m-30) REVERT: H 69 ASP cc_start: 0.6750 (p0) cc_final: 0.6445 (p0) REVERT: I 35 MET cc_start: 0.8021 (mmt) cc_final: 0.7608 (mmm) REVERT: I 36 LYS cc_start: 0.8474 (mppt) cc_final: 0.7985 (mppt) REVERT: I 42 ILE cc_start: 0.8959 (mt) cc_final: 0.8434 (mt) REVERT: I 43 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7548 (mmtm) REVERT: J 17 ASP cc_start: 0.8839 (t0) cc_final: 0.8518 (t0) REVERT: J 46 LYS cc_start: 0.8562 (tptm) cc_final: 0.8174 (tptt) REVERT: L 54 PHE cc_start: 0.6773 (t80) cc_final: 0.6306 (t80) REVERT: O 47 PHE cc_start: 0.5840 (OUTLIER) cc_final: 0.5086 (t80) REVERT: O 60 MET cc_start: 0.4024 (ttt) cc_final: 0.1648 (mmp) REVERT: Q 60 MET cc_start: 0.2689 (ptm) cc_final: 0.2087 (mmp) REVERT: R 49 TYR cc_start: 0.8062 (m-80) cc_final: 0.7707 (m-80) REVERT: S 44 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8522 (tp-100) REVERT: S 151 GLU cc_start: 0.7647 (mp0) cc_final: 0.7390 (mp0) REVERT: S 180 GLN cc_start: 0.8526 (mp10) cc_final: 0.8275 (mp10) REVERT: a 1 MET cc_start: 0.1338 (ttt) cc_final: -0.1309 (pmm) REVERT: a 5 LEU cc_start: 0.4270 (OUTLIER) cc_final: 0.3274 (mp) REVERT: a 43 VAL cc_start: 0.6666 (t) cc_final: 0.6384 (p) REVERT: a 73 MET cc_start: 0.4118 (mmm) cc_final: 0.3833 (mmm) REVERT: a 104 MET cc_start: 0.2985 (mpp) cc_final: 0.2437 (ptt) REVERT: a 202 LEU cc_start: 0.5387 (mt) cc_final: 0.4798 (pp) REVERT: b 11 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.4189 (tptt) REVERT: b 125 PHE cc_start: 0.3566 (m-80) cc_final: 0.2349 (p90) REVERT: b 129 ARG cc_start: 0.5584 (mmt-90) cc_final: 0.4834 (mtm180) REVERT: b 156 ASP cc_start: 0.7619 (m-30) cc_final: 0.7377 (m-30) REVERT: b 165 MET cc_start: 0.8262 (ptp) cc_final: 0.7679 (mmm) REVERT: b 166 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7066 (ttp-110) REVERT: g 70 LYS cc_start: -0.1194 (OUTLIER) cc_final: -0.2401 (mttt) REVERT: h 36 GLN cc_start: 0.7934 (tp40) cc_final: 0.7282 (tp40) REVERT: h 40 ASP cc_start: 0.8468 (m-30) cc_final: 0.7958 (m-30) REVERT: h 47 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8683 (mttp) outliers start: 151 outliers final: 114 residues processed: 562 average time/residue: 0.2405 time to fit residues: 224.1517 Evaluate side-chains 569 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 440 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 18 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 140 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain b residue 164 MET Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain j residue 11 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 166 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 297 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 495 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 436 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN a 172 HIS a 223 HIS b 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.183305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.135833 restraints weight = 52683.285| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.39 r_work: 0.3406 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39714 Z= 0.138 Angle : 0.568 13.887 53733 Z= 0.286 Chirality : 0.042 0.232 6271 Planarity : 0.004 0.058 6863 Dihedral : 6.743 86.631 5698 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.46 % Allowed : 19.83 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 5053 helix: 1.83 (0.10), residues: 2634 sheet: 0.41 (0.22), residues: 563 loop : -0.90 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 337 TYR 0.044 0.001 TYR D 345 PHE 0.028 0.001 PHE E 424 TRP 0.027 0.001 TRP d 53 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00323 (39708) covalent geometry : angle 0.56827 (53733) hydrogen bonds : bond 0.04266 ( 2233) hydrogen bonds : angle 4.22007 ( 6546) Misc. bond : bond 0.00242 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 446 time to evaluate : 1.483 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: A 173 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 224 ASP cc_start: 0.8590 (t0) cc_final: 0.8235 (t0) REVERT: B 27 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: B 210 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7036 (ttp-170) REVERT: B 488 LYS cc_start: 0.9064 (ptmt) cc_final: 0.8612 (ttmm) REVERT: C 62 MET cc_start: 0.7565 (ttm) cc_final: 0.7296 (ttp) REVERT: C 245 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8046 (tp) REVERT: C 477 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7506 (tm-30) REVERT: C 496 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8639 (mtmm) REVERT: C 497 LEU cc_start: 0.8442 (tp) cc_final: 0.8100 (tp) REVERT: D 52 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.7563 (m90) REVERT: D 200 MET cc_start: 0.8357 (tpp) cc_final: 0.8044 (tpp) REVERT: E 428 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8352 (mm) REVERT: F 95 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8273 (ttm) REVERT: F 292 MET cc_start: 0.8692 (tmm) cc_final: 0.8314 (tmm) REVERT: G 15 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8654 (m-40) REVERT: G 140 ASP cc_start: 0.8354 (m-30) cc_final: 0.7831 (m-30) REVERT: H 69 ASP cc_start: 0.6775 (p0) cc_final: 0.6555 (p0) REVERT: I 35 MET cc_start: 0.7857 (mmt) cc_final: 0.7159 (mmt) REVERT: I 36 LYS cc_start: 0.8547 (mppt) cc_final: 0.8041 (mppt) REVERT: I 42 ILE cc_start: 0.9031 (mt) cc_final: 0.8637 (mt) REVERT: I 43 LYS cc_start: 0.7889 (mmtm) cc_final: 0.7556 (mmtm) REVERT: J 17 ASP cc_start: 0.8888 (t0) cc_final: 0.8562 (t0) REVERT: J 46 LYS cc_start: 0.8565 (tptm) cc_final: 0.8156 (tptt) REVERT: L 54 PHE cc_start: 0.6853 (t80) cc_final: 0.6337 (t80) REVERT: M 2 ILE cc_start: 0.5214 (OUTLIER) cc_final: 0.4965 (mt) REVERT: O 60 MET cc_start: 0.4083 (ttt) cc_final: 0.1678 (mmp) REVERT: R 49 TYR cc_start: 0.8166 (m-80) cc_final: 0.7812 (m-80) REVERT: S 44 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8523 (tp-100) REVERT: S 109 MET cc_start: 0.8446 (mmm) cc_final: 0.8040 (mmm) REVERT: S 151 GLU cc_start: 0.7674 (mp0) cc_final: 0.7444 (mp0) REVERT: S 180 GLN cc_start: 0.8544 (mp10) cc_final: 0.8299 (mp10) REVERT: a 1 MET cc_start: 0.1197 (ttt) cc_final: -0.1395 (pmm) REVERT: a 5 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3298 (mp) REVERT: a 31 PHE cc_start: 0.3705 (t80) cc_final: 0.3146 (t80) REVERT: a 58 MET cc_start: 0.5664 (mmm) cc_final: 0.5220 (tpp) REVERT: a 73 MET cc_start: 0.4171 (mmm) cc_final: 0.3879 (mmm) REVERT: a 104 MET cc_start: 0.2981 (mpp) cc_final: 0.2438 (ptt) REVERT: a 202 LEU cc_start: 0.5470 (mt) cc_final: 0.4899 (pp) REVERT: b 7 GLU cc_start: 0.5783 (tm-30) cc_final: 0.4768 (tp30) REVERT: b 11 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4177 (tptt) REVERT: b 125 PHE cc_start: 0.3643 (m-80) cc_final: 0.2400 (p90) REVERT: b 129 ARG cc_start: 0.5585 (mmt-90) cc_final: 0.4849 (mtm180) REVERT: b 156 ASP cc_start: 0.7657 (m-30) cc_final: 0.7378 (m-30) REVERT: b 165 MET cc_start: 0.8236 (ptp) cc_final: 0.7636 (mmm) REVERT: b 166 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7081 (ttp-110) REVERT: g 70 LYS cc_start: -0.1091 (OUTLIER) cc_final: -0.2354 (mttt) REVERT: h 36 GLN cc_start: 0.7913 (tp40) cc_final: 0.7245 (tp40) REVERT: h 40 ASP cc_start: 0.8311 (m-30) cc_final: 0.7763 (m-30) REVERT: h 47 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8740 (mttp) outliers start: 140 outliers final: 108 residues processed: 550 average time/residue: 0.2403 time to fit residues: 218.0703 Evaluate side-chains 555 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 434 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 140 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 399 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 401 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 391 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 420 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 32 ASN C 78 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS a 223 HIS b 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.183309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.135144 restraints weight = 52956.820| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.30 r_work: 0.3415 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39714 Z= 0.134 Angle : 0.571 13.774 53733 Z= 0.287 Chirality : 0.042 0.229 6271 Planarity : 0.004 0.082 6863 Dihedral : 6.652 82.976 5698 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.65 % Allowed : 19.56 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 5053 helix: 1.83 (0.10), residues: 2644 sheet: 0.42 (0.22), residues: 563 loop : -0.90 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 337 TYR 0.044 0.001 TYR D 345 PHE 0.028 0.001 PHE E 424 TRP 0.027 0.001 TRP d 53 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00311 (39708) covalent geometry : angle 0.57114 (53733) hydrogen bonds : bond 0.04222 ( 2233) hydrogen bonds : angle 4.20892 ( 6546) Misc. bond : bond 0.00233 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 444 time to evaluate : 1.504 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: A 173 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 224 ASP cc_start: 0.8588 (t0) cc_final: 0.8241 (t0) REVERT: B 27 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: B 210 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7023 (ttp-170) REVERT: B 399 GLU cc_start: 0.8642 (tp30) cc_final: 0.8380 (mt-10) REVERT: B 488 LYS cc_start: 0.9062 (ptmt) cc_final: 0.8602 (ttmm) REVERT: C 62 MET cc_start: 0.7490 (ttm) cc_final: 0.7232 (ttp) REVERT: C 245 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8043 (tp) REVERT: C 477 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7502 (tm-30) REVERT: C 496 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8647 (mtmm) REVERT: C 497 LEU cc_start: 0.8434 (tp) cc_final: 0.8095 (tp) REVERT: D 52 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.7513 (m90) REVERT: D 200 MET cc_start: 0.8348 (tpp) cc_final: 0.8031 (tpp) REVERT: E 428 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8367 (mm) REVERT: F 95 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8255 (ttm) REVERT: F 292 MET cc_start: 0.8683 (tmm) cc_final: 0.8297 (tmm) REVERT: G 15 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8654 (m-40) REVERT: G 140 ASP cc_start: 0.8366 (m-30) cc_final: 0.7829 (m-30) REVERT: H 69 ASP cc_start: 0.6843 (p0) cc_final: 0.6624 (p0) REVERT: I 35 MET cc_start: 0.7868 (mmt) cc_final: 0.7114 (mmt) REVERT: I 36 LYS cc_start: 0.8548 (mppt) cc_final: 0.8031 (mppt) REVERT: I 42 ILE cc_start: 0.9056 (mt) cc_final: 0.8666 (mt) REVERT: I 43 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7578 (mmtm) REVERT: J 17 ASP cc_start: 0.8865 (t0) cc_final: 0.8543 (t0) REVERT: J 46 LYS cc_start: 0.8530 (tptm) cc_final: 0.8145 (tptt) REVERT: L 54 PHE cc_start: 0.6861 (t80) cc_final: 0.6282 (t80) REVERT: M 2 ILE cc_start: 0.5202 (OUTLIER) cc_final: 0.4961 (mt) REVERT: N 28 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6318 (t) REVERT: O 60 MET cc_start: 0.4168 (ttt) cc_final: 0.1680 (mmp) REVERT: Q 60 MET cc_start: 0.1975 (mtp) cc_final: 0.1028 (mmp) REVERT: R 49 TYR cc_start: 0.8147 (m-80) cc_final: 0.7849 (m-80) REVERT: S 44 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8530 (tp-100) REVERT: S 109 MET cc_start: 0.8535 (mmm) cc_final: 0.8186 (mmm) REVERT: S 180 GLN cc_start: 0.8538 (mp10) cc_final: 0.8290 (mp10) REVERT: a 1 MET cc_start: 0.1215 (ttt) cc_final: -0.1167 (pmm) REVERT: a 5 LEU cc_start: 0.4390 (OUTLIER) cc_final: 0.3326 (mp) REVERT: a 49 MET cc_start: 0.6600 (ttp) cc_final: 0.6264 (ttm) REVERT: a 73 MET cc_start: 0.4162 (mmm) cc_final: 0.3898 (mmm) REVERT: a 104 MET cc_start: 0.3018 (mpp) cc_final: 0.2484 (mmm) REVERT: a 202 LEU cc_start: 0.5462 (mt) cc_final: 0.4901 (pp) REVERT: b 11 LYS cc_start: 0.5450 (OUTLIER) cc_final: 0.4183 (tptt) REVERT: b 125 PHE cc_start: 0.3643 (m-80) cc_final: 0.2417 (p90) REVERT: b 129 ARG cc_start: 0.5971 (mmt-90) cc_final: 0.4966 (mtm180) REVERT: b 156 ASP cc_start: 0.7621 (m-30) cc_final: 0.7334 (m-30) REVERT: b 165 MET cc_start: 0.8233 (ptp) cc_final: 0.7856 (mmt) REVERT: b 166 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7089 (ttp-110) REVERT: g 70 LYS cc_start: -0.1184 (OUTLIER) cc_final: -0.2458 (mttt) REVERT: h 18 TYR cc_start: 0.7026 (t80) cc_final: 0.6681 (t80) REVERT: h 22 ARG cc_start: 0.6699 (ptt180) cc_final: 0.6194 (ttp80) REVERT: h 36 GLN cc_start: 0.7957 (tp40) cc_final: 0.7536 (tp40) REVERT: h 40 ASP cc_start: 0.8482 (m-30) cc_final: 0.8256 (m-30) REVERT: h 47 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8723 (mttp) REVERT: h 49 MET cc_start: 0.7805 (tmm) cc_final: 0.7402 (ttp) REVERT: h 50 TYR cc_start: 0.5408 (m-80) cc_final: 0.5064 (m-80) REVERT: j 17 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6352 (m-80) outliers start: 148 outliers final: 122 residues processed: 555 average time/residue: 0.2389 time to fit residues: 219.1265 Evaluate side-chains 572 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 435 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain I residue 3 TYR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 140 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 17 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 414 optimal weight: 0.0020 chunk 438 optimal weight: 0.8980 chunk 193 optimal weight: 0.2980 chunk 338 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 448 optimal weight: 7.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 HIS a 223 HIS b 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.182623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134080 restraints weight = 52676.958| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.29 r_work: 0.3406 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39714 Z= 0.146 Angle : 0.587 13.592 53733 Z= 0.295 Chirality : 0.043 0.249 6271 Planarity : 0.004 0.073 6863 Dihedral : 6.610 82.194 5698 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.65 % Allowed : 19.70 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.12), residues: 5053 helix: 1.80 (0.10), residues: 2644 sheet: 0.35 (0.22), residues: 565 loop : -0.96 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 337 TYR 0.048 0.001 TYR D 345 PHE 0.027 0.001 PHE d 15 TRP 0.035 0.001 TRP d 53 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00346 (39708) covalent geometry : angle 0.58723 (53733) hydrogen bonds : bond 0.04345 ( 2233) hydrogen bonds : angle 4.23093 ( 6546) Misc. bond : bond 0.00245 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10106 Ramachandran restraints generated. 5053 Oldfield, 0 Emsley, 5053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 440 time to evaluate : 1.334 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: A 173 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8575 (p) REVERT: A 224 ASP cc_start: 0.8524 (t0) cc_final: 0.8170 (t0) REVERT: B 27 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: B 210 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7021 (ttp-170) REVERT: B 399 GLU cc_start: 0.8633 (tp30) cc_final: 0.8323 (mt-10) REVERT: B 488 LYS cc_start: 0.9056 (ptmt) cc_final: 0.8582 (ttmm) REVERT: C 62 MET cc_start: 0.7568 (ttm) cc_final: 0.7307 (ttp) REVERT: C 245 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8039 (tp) REVERT: C 477 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7484 (tm-30) REVERT: C 496 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8661 (mtmm) REVERT: D 52 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.7516 (m90) REVERT: D 200 MET cc_start: 0.8342 (tpp) cc_final: 0.8022 (tpp) REVERT: E 428 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (mm) REVERT: F 95 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8313 (ttm) REVERT: F 292 MET cc_start: 0.8712 (tmm) cc_final: 0.8301 (tmm) REVERT: G 15 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8644 (m-40) REVERT: G 140 ASP cc_start: 0.8290 (m-30) cc_final: 0.7773 (m-30) REVERT: H 69 ASP cc_start: 0.6856 (p0) cc_final: 0.6506 (p0) REVERT: H 136 GLU cc_start: 0.8303 (pt0) cc_final: 0.8014 (pt0) REVERT: I 35 MET cc_start: 0.7963 (mmt) cc_final: 0.7173 (mmt) REVERT: I 36 LYS cc_start: 0.8512 (mppt) cc_final: 0.7988 (mppt) REVERT: I 42 ILE cc_start: 0.9128 (mt) cc_final: 0.8757 (mt) REVERT: I 43 LYS cc_start: 0.7886 (mmtm) cc_final: 0.7567 (mmtm) REVERT: J 17 ASP cc_start: 0.8818 (t0) cc_final: 0.8471 (t0) REVERT: J 46 LYS cc_start: 0.8495 (tptm) cc_final: 0.8109 (tptt) REVERT: L 54 PHE cc_start: 0.6847 (t80) cc_final: 0.6248 (t80) REVERT: M 2 ILE cc_start: 0.5277 (OUTLIER) cc_final: 0.5012 (mt) REVERT: N 28 VAL cc_start: 0.6546 (OUTLIER) cc_final: 0.6323 (t) REVERT: O 60 MET cc_start: 0.4160 (ttt) cc_final: 0.1625 (mmp) REVERT: Q 60 MET cc_start: 0.1981 (mtp) cc_final: 0.1051 (mmp) REVERT: R 49 TYR cc_start: 0.7527 (m-80) cc_final: 0.7183 (m-80) REVERT: S 44 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8551 (tp-100) REVERT: S 109 MET cc_start: 0.8547 (mmm) cc_final: 0.8182 (mmm) REVERT: S 180 GLN cc_start: 0.8534 (mp10) cc_final: 0.8272 (mp10) REVERT: a 1 MET cc_start: 0.1183 (ttt) cc_final: -0.1202 (pmm) REVERT: a 5 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.3348 (mp) REVERT: a 49 MET cc_start: 0.6570 (ttp) cc_final: 0.6257 (ttm) REVERT: a 73 MET cc_start: 0.4164 (mmm) cc_final: 0.3934 (mmm) REVERT: a 104 MET cc_start: 0.3081 (mpp) cc_final: 0.2540 (mmm) REVERT: a 202 LEU cc_start: 0.5465 (mt) cc_final: 0.4901 (pp) REVERT: b 11 LYS cc_start: 0.5484 (OUTLIER) cc_final: 0.4198 (tptt) REVERT: b 125 PHE cc_start: 0.3633 (m-80) cc_final: 0.2416 (p90) REVERT: b 129 ARG cc_start: 0.5949 (mmt-90) cc_final: 0.4953 (mtm180) REVERT: b 156 ASP cc_start: 0.7639 (m-30) cc_final: 0.7350 (m-30) REVERT: b 165 MET cc_start: 0.8258 (ptp) cc_final: 0.7662 (mmm) REVERT: b 166 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7065 (ttp-110) REVERT: g 70 LYS cc_start: -0.1128 (OUTLIER) cc_final: -0.2388 (mttt) REVERT: h 18 TYR cc_start: 0.7026 (t80) cc_final: 0.6725 (t80) REVERT: h 22 ARG cc_start: 0.6579 (ptt180) cc_final: 0.6116 (ttp80) REVERT: h 36 GLN cc_start: 0.7928 (tp40) cc_final: 0.7495 (tp40) REVERT: h 40 ASP cc_start: 0.8411 (m-30) cc_final: 0.8207 (m-30) REVERT: h 47 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8716 (mttp) REVERT: h 50 TYR cc_start: 0.5341 (m-80) cc_final: 0.4977 (m-80) REVERT: j 17 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6368 (m-80) outliers start: 148 outliers final: 124 residues processed: 552 average time/residue: 0.2377 time to fit residues: 216.7448 Evaluate side-chains 568 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 429 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 52 HIS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 54 PHE Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 118 CYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 140 MET Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 223 HIS Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 160 SER Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 19 ILE Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 56 TYR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 17 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 248 optimal weight: 0.5980 chunk 274 optimal weight: 0.4980 chunk 331 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 486 optimal weight: 0.9980 chunk 475 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 415 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 GLN a 172 HIS a 223 HIS b 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.186646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140719 restraints weight = 52875.680| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.57 r_work: 0.3426 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 39714 Z= 0.111 Angle : 0.560 13.487 53733 Z= 0.281 Chirality : 0.042 0.231 6271 Planarity : 0.004 0.066 6863 Dihedral : 6.409 82.101 5698 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.91 % Allowed : 20.64 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 5053 helix: 1.89 (0.10), residues: 2645 sheet: 0.48 (0.22), residues: 566 loop : -0.87 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 337 TYR 0.038 0.001 TYR D 345 PHE 0.027 0.001 PHE E 424 TRP 0.048 0.001 TRP d 53 HIS 0.007 0.001 HIS a 223 Details of bonding type rmsd covalent geometry : bond 0.00241 (39708) covalent geometry : angle 0.56045 (53733) hydrogen bonds : bond 0.03856 ( 2233) hydrogen bonds : angle 4.12961 ( 6546) Misc. bond : bond 0.00190 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13914.12 seconds wall clock time: 237 minutes 29.13 seconds (14249.13 seconds total)