Starting phenix.real_space_refine on Tue Sep 15 09:24:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.cif" model { file = "/net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cp6_7548/09_2026/6cp6_7548.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 92 5.16 5 C 24827 2.51 5 N 6557 2.21 5 O 7364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38853 Number of models: 1 Model: "" Number of chains: 32 Chain: "K" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 523 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1333 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3830 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3861 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3549 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 448} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2086 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1221 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1357 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1760 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.50, per 1000 atoms: 0.19 Number of scatterers: 38853 At special positions: 0 Unit cell: (125.46, 151.29, 244.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 13 15.00 O 7364 8.00 N 6557 7.00 C 24827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9376 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 27 sheets defined 58.7% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'K' and resid 2 through 15 removed outlier: 3.851A pdb=" N ALA K 6 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 40 removed outlier: 3.654A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE K 28 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 74 Proline residue: K 49 - end of helix removed outlier: 3.609A pdb=" N ALA K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY K 62 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU K 66 " --> pdb=" O GLY K 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 16 through 18 No H-bonds generated for 'chain 'L' and resid 16 through 18' Processing helix chain 'L' and resid 19 through 24 Processing helix chain 'L' and resid 24 through 39 removed outlier: 3.566A pdb=" N VAL L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 44 Processing helix chain 'L' and resid 47 through 74 removed outlier: 3.842A pdb=" N LEU L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 Processing helix chain 'M' and resid 16 through 18 No H-bonds generated for 'chain 'M' and resid 16 through 18' Processing helix chain 'M' and resid 19 through 24 Processing helix chain 'M' and resid 24 through 38 Processing helix chain 'M' and resid 43 through 74 Proline residue: M 49 - end of helix removed outlier: 3.788A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS M 65 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 66 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 removed outlier: 4.074A pdb=" N ALA N 6 " --> pdb=" O GLN N 2 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER N 15 " --> pdb=" O GLY N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 18 No H-bonds generated for 'chain 'N' and resid 16 through 18' Processing helix chain 'N' and resid 19 through 38 removed outlier: 4.543A pdb=" N ALA N 27 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 Proline residue: N 49 - end of helix removed outlier: 4.364A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 removed outlier: 3.920A pdb=" N ALA O 6 " --> pdb=" O GLN O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 18 No H-bonds generated for 'chain 'O' and resid 16 through 18' Processing helix chain 'O' and resid 19 through 38 removed outlier: 3.699A pdb=" N ALA O 27 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 42 No H-bonds generated for 'chain 'O' and resid 40 through 42' Processing helix chain 'O' and resid 43 through 57 Proline residue: O 49 - end of helix removed outlier: 3.716A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 3.699A pdb=" N GLY O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS O 65 " --> pdb=" O THR O 61 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 removed outlier: 4.024A pdb=" N ALA P 6 " --> pdb=" O GLN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 40 removed outlier: 3.860A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 74 removed outlier: 3.781A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 18 through 40 removed outlier: 3.877A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 74 removed outlier: 3.969A pdb=" N MET Q 50 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 Processing helix chain 'R' and resid 16 through 18 No H-bonds generated for 'chain 'R' and resid 16 through 18' Processing helix chain 'R' and resid 19 through 39 removed outlier: 4.634A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 43 through 75 Proline residue: R 49 - end of helix removed outlier: 3.673A pdb=" N LEU R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS R 65 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 73 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE R 74 " --> pdb=" O PHE R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 17 removed outlier: 4.424A pdb=" N ILE S 17 " --> pdb=" O GLY S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 38 removed outlier: 3.741A pdb=" N ALA S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY S 25 " --> pdb=" O GLY S 21 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.549A pdb=" N ILE S 43 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 40 through 44' Processing helix chain 'S' and resid 46 through 63 removed outlier: 4.299A pdb=" N MET S 50 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 74 removed outlier: 3.726A pdb=" N LEU S 72 " --> pdb=" O VAL S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 16 through 18 No H-bonds generated for 'chain 'T' and resid 16 through 18' Processing helix chain 'T' and resid 19 through 38 removed outlier: 4.457A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 42 No H-bonds generated for 'chain 'T' and resid 40 through 42' Processing helix chain 'T' and resid 43 through 62 removed outlier: 3.758A pdb=" N PHE T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.645A pdb=" N GLY T 62 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 72 Processing helix chain 'Y' and resid 17 through 28 Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Y' and resid 32 through 50 Processing helix chain 'Y' and resid 64 through 77 Processing helix chain 'Y' and resid 83 through 95 removed outlier: 4.598A pdb=" N ASN Y 87 " --> pdb=" O GLY Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 117 Processing helix chain 'Y' and resid 130 through 144 Processing helix chain 'Y' and resid 180 through 191 removed outlier: 3.694A pdb=" N LEU Y 191 " --> pdb=" O LEU Y 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.603A pdb=" N GLU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.752A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.531A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 261 Proline residue: A 249 - end of helix removed outlier: 3.618A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 298 No H-bonds generated for 'chain 'A' and resid 297 through 298' Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.677A pdb=" N GLU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.774A pdb=" N PHE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.563A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 403 removed outlier: 3.974A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.632A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 462 through 478 Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 510 Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.596A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.678A pdb=" N VAL B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.670A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.672A pdb=" N PHE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.650A pdb=" N GLN B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.858A pdb=" N LYS B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix removed outlier: 3.514A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 3.772A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 508 removed outlier: 3.739A pdb=" N PHE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.615A pdb=" N GLU C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.707A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 261 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.941A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 297 through 298 No H-bonds generated for 'chain 'C' and resid 297 through 298' Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 338 through 346 removed outlier: 3.600A pdb=" N SER C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.720A pdb=" N PHE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 4.083A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 391 through 408 removed outlier: 4.001A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix removed outlier: 3.755A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 removed outlier: 3.616A pdb=" N SER C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.529A pdb=" N GLY D 205 " --> pdb=" O MET D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 246 removed outlier: 5.107A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 removed outlier: 3.958A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 295 removed outlier: 3.604A pdb=" N ASP D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 326 removed outlier: 4.136A pdb=" N THR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 4.754A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 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 446 Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 231 through 246 Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 277 through 281 removed outlier: 3.789A pdb=" N GLY E 280 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.740A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 326 Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.954A pdb=" N SER E 340 " --> pdb=" O SER E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 391 removed outlier: 7.450A pdb=" N GLN E 365 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N GLU E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 removed outlier: 3.748A pdb=" N GLU E 395 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 414 removed outlier: 3.581A pdb=" N THR E 403 " --> pdb=" O GLN E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.609A pdb=" N TYR E 458 " --> pdb=" O HIS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 477 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 246 Processing helix chain 'F' and resid 257 through 270 removed outlier: 3.807A pdb=" N PHE F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 327 removed outlier: 4.004A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 364 through 391 removed outlier: 4.803A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 removed outlier: 3.719A pdb=" N GLU F 395 " --> pdb=" O GLY F 392 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 396 " --> pdb=" O MET F 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 392 through 396' Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.779A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 477 Processing helix chain 'G' and resid 2 through 55 removed outlier: 4.091A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 102 removed outlier: 3.783A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 removed outlier: 3.731A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 154 Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.743A pdb=" N PHE G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY G 195 " --> pdb=" O PRO G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 195' Processing helix chain 'G' and resid 200 through 203 removed outlier: 3.990A pdb=" N ALA G 203 " --> pdb=" O ASP G 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 203' Processing helix chain 'G' and resid 204 through 276 removed outlier: 4.402A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 removed outlier: 3.524A pdb=" N LEU H 104 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 138 removed outlier: 3.850A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 24 Processing helix chain 'I' and resid 31 through 38 Processing helix chain 'Z' and resid 55 through 112 removed outlier: 4.881A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.628A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 133 removed outlier: 3.602A pdb=" N THR Z 119 " --> pdb=" O ASN Z 115 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP Z 125 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 185 removed outlier: 3.570A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY Z 185 " --> pdb=" O GLN Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 205 removed outlier: 4.252A pdb=" N VAL Z 193 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 19 Processing helix chain '7' and resid 26 through 48 Processing helix chain '7' and resid 57 through 62 removed outlier: 4.149A pdb=" N LEU 7 62 " --> pdb=" O TYR 7 58 " (cutoff:3.500A) Processing helix chain '7' and resid 67 through 78 Processing helix chain '7' and resid 90 through 127 removed outlier: 3.522A pdb=" N SER 7 94 " --> pdb=" O GLN 7 90 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 142 through 156 removed outlier: 4.157A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 17 Processing helix chain '6' and resid 18 through 23 Processing helix chain '6' and resid 42 through 45 removed outlier: 3.624A pdb=" N GLN 6 45 " --> pdb=" O LEU 6 42 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 42 through 45' Processing helix chain '6' and resid 46 through 51 Processing helix chain '6' and resid 77 through 92 Processing helix chain 'U' and resid 17 through 32 removed outlier: 3.724A pdb=" N ALA U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS U 32 " --> pdb=" O VAL U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 56 removed outlier: 3.652A pdb=" N LYS U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 85 removed outlier: 3.929A pdb=" N TYR U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain '8' and resid 8 through 31 Processing helix chain '8' and resid 32 through 48 removed outlier: 4.123A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 42 Processing helix chain 'X' and resid 56 through 77 removed outlier: 3.890A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE X 77 " --> pdb=" O THR X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 84 No H-bonds generated for 'chain 'X' and resid 82 through 84' Processing helix chain 'X' and resid 85 through 100 removed outlier: 3.890A pdb=" N PHE X 93 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE X 95 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 137 Processing helix chain 'X' and resid 139 through 146 removed outlier: 3.596A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL X 146 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 153 No H-bonds generated for 'chain 'X' and resid 151 through 153' Processing helix chain 'X' and resid 154 through 175 removed outlier: 3.687A pdb=" N VAL X 159 " --> pdb=" O VAL X 155 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE X 167 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA X 168 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU X 173 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 199 removed outlier: 4.032A pdb=" N LEU X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU X 187 " --> pdb=" O ALA X 183 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA X 192 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 207 Processing helix chain 'X' and resid 210 through 247 removed outlier: 4.403A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 32 removed outlier: 3.742A pdb=" N PHE J 17 " --> pdb=" O TYR J 13 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 122 through 124 removed outlier: 3.841A pdb=" N THR Y 175 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 27 " --> pdb=" O THR Y 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.103A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN A 95 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU A 56 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 93 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.396A pdb=" N ARG A 108 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA A 235 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 202 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 269 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 204 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 271 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 206 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.869A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.546A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 17 current: chain 'B' and resid 91 through 96 Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.546A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 62 through 68 current: chain 'F' and resid 36 through 41 removed outlier: 5.734A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 17 current: chain 'B' and resid 91 through 96 Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.587A pdb=" N VAL B 110 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 37 removed outlier: 6.649A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN C 95 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU C 56 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR C 93 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB4, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.639A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.737A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 17 removed outlier: 5.607A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.525A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS D 152 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.044A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.235A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.426A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS E 152 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.290A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC6, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.862A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.073A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 176 through 183 removed outlier: 3.869A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN G 131 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 22 through 27 removed outlier: 5.003A pdb=" N SER H 23 " --> pdb=" O PHE H 14 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE H 14 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY H 72 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU H 53 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE H 74 " --> pdb=" O GLN H 51 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN H 51 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR H 76 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL H 49 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 2177 hydrogen bonds defined for protein. 6321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.49 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6560 1.31 - 1.43: 9444 1.43 - 1.56: 23285 1.56 - 1.68: 24 1.68 - 1.81: 168 Bond restraints: 39481 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.34e+01 ... (remaining 39476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 53170 4.82 - 9.65: 320 9.65 - 14.47: 11 14.47 - 19.29: 0 19.29 - 24.12: 6 Bond angle restraints: 53507 Sorted by residual: angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 112.71 24.12 1.00e+00 1.00e+00 5.82e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 113.25 23.58 1.00e+00 1.00e+00 5.56e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.20 21.67 1.00e+00 1.00e+00 4.69e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.64 21.23 1.00e+00 1.00e+00 4.51e+02 ... (remaining 53502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 23484 33.93 - 67.87: 246 67.87 - 101.80: 24 101.80 - 135.73: 1 135.73 - 169.67: 1 Dihedral angle restraints: 23756 sinusoidal: 9153 harmonic: 14603 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual 300.00 130.34 169.67 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 177.34 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" CA PHE R 55 " pdb=" C PHE R 55 " pdb=" N ALA R 56 " pdb=" CA ALA R 56 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 23753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5865 0.097 - 0.193: 467 0.193 - 0.290: 15 0.290 - 0.386: 1 0.386 - 0.483: 1 Chirality restraints: 6349 Sorted by residual: chirality pdb=" CB ILE U 5 " pdb=" CA ILE U 5 " pdb=" CG1 ILE U 5 " pdb=" CG2 ILE U 5 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CB ILE P 43 " pdb=" CA ILE P 43 " pdb=" CG1 ILE P 43 " pdb=" CG2 ILE P 43 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CB ILE Q 14 " pdb=" CA ILE Q 14 " pdb=" CG1 ILE Q 14 " pdb=" CG2 ILE Q 14 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 6346 not shown) Planarity restraints: 6839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 6 17 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO 6 18 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO 6 18 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO 6 18 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO D 322 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 53 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LEU R 53 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU R 53 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY R 54 " -0.017 2.00e-02 2.50e+03 ... (remaining 6836 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3593 2.74 - 3.28: 41043 3.28 - 3.82: 69750 3.82 - 4.36: 81788 4.36 - 4.90: 133048 Nonbonded interactions: 329222 Sorted by model distance: nonbonded pdb=" O GLY Y 172 " pdb=" OD1 ASP Y 173 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP B 172 " pdb=" OG1 THR B 331 " model vdw 2.235 3.040 nonbonded pdb=" O VAL E 87 " pdb=" OG SER E 111 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP Y 193 " pdb=" N SER Y 194 " model vdw 2.246 3.120 nonbonded pdb=" CB GLU B 29 " pdb=" CG ARG B 92 " model vdw 2.255 3.840 ... (remaining 329217 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 4 through 18 or resid 20 through 22 or (resid 23 and (name \ N or name CA or name C or name O or name CB )) or resid 24 through 28 or (resid \ 29 and (name N or name CA or name C or name O or name CB )) or resid 30 through \ 509 or resid 600)) selection = chain 'B' selection = (chain 'C' and (resid 4 through 18 or resid 20 through 22 or (resid 23 and (name \ N or name CA or name C or name O or name CB )) or resid 24 through 509 or resid \ 600)) } ncs_group { reference = (chain 'D' and resid 7 through 475) selection = (chain 'E' and resid 7 through 475) selection = (chain 'F' and resid 7 through 475) } ncs_group { reference = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'L' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 74)) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'N' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 74)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = chain 'Q' selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'S' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 74)) selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.330 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 0.090 39481 Z= 0.360 Angle : 1.088 24.118 53507 Z= 0.648 Chirality : 0.054 0.483 6349 Planarity : 0.007 0.086 6839 Dihedral : 10.804 169.666 14380 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.17 % Rotamer: Outliers : 0.66 % Allowed : 4.03 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -3.06 (0.10), residues: 5060 helix: -2.04 (0.08), residues: 2508 sheet: -1.67 (0.21), residues: 568 loop : -1.88 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 114 TYR 0.028 0.003 TYR 7 58 PHE 0.035 0.003 PHE 7 95 TRP 0.028 0.003 TRP A 258 HIS 0.020 0.003 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.36 (39481) covalent geometry : angle 1.08794 / 0.65 (53507) hydrogen bonds : bond 0.17936 / 11.80 ( 2169) hydrogen bonds : angle 7.92557 / 5.57 ( 6321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 1168 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 19 LEU cc_start: 0.4059 (pp) cc_final: 0.2789 (mt) REVERT: K 43 ILE cc_start: 0.7698 (tp) cc_final: 0.7211 (tt) REVERT: K 53 LEU cc_start: 0.8160 (tm) cc_final: 0.7745 (mt) REVERT: K 61 THR cc_start: 0.6798 (p) cc_final: 0.6513 (p) REVERT: M 46 THR cc_start: 0.6797 (m) cc_final: 0.6513 (m) REVERT: M 50 MET cc_start: 0.8248 (mtm) cc_final: 0.7951 (tpp) REVERT: N 29 VAL cc_start: 0.8391 (t) cc_final: 0.8012 (t) REVERT: N 30 PHE cc_start: 0.7615 (m-80) cc_final: 0.7177 (m-80) REVERT: N 67 MET cc_start: 0.5001 (pp-130) cc_final: 0.4698 (ttt) REVERT: N 70 PHE cc_start: 0.6687 (t80) cc_final: 0.6432 (t80) REVERT: O 16 THR cc_start: 0.4051 (m) cc_final: 0.3721 (m) REVERT: P 5 LEU cc_start: 0.8510 (pt) cc_final: 0.8282 (tp) REVERT: P 39 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7258 (mtp180) REVERT: P 47 VAL cc_start: 0.7906 (m) cc_final: 0.7588 (m) REVERT: P 67 MET cc_start: 0.6089 (pp-130) cc_final: 0.5786 (ppp) REVERT: Q 63 LEU cc_start: 0.7625 (mt) cc_final: 0.7393 (tt) REVERT: Q 67 MET cc_start: 0.3905 (pp-130) cc_final: 0.3546 (ptp) REVERT: Q 68 VAL cc_start: 0.8410 (t) cc_final: 0.8185 (t) REVERT: R 4 VAL cc_start: 0.3447 (p) cc_final: 0.2919 (t) REVERT: R 34 ILE cc_start: 0.8372 (mt) cc_final: 0.8028 (mm) REVERT: R 53 LEU cc_start: 0.8114 (tm) cc_final: 0.7861 (mt) REVERT: R 72 LEU cc_start: 0.6239 (tp) cc_final: 0.5929 (tp) REVERT: S 5 LEU cc_start: 0.8281 (pt) cc_final: 0.7923 (pt) REVERT: S 45 ASP cc_start: 0.8853 (m-30) cc_final: 0.8381 (t0) REVERT: S 47 VAL cc_start: 0.8653 (m) cc_final: 0.8416 (p) REVERT: S 70 PHE cc_start: 0.8147 (m-10) cc_final: 0.7777 (m-80) REVERT: S 72 LEU cc_start: 0.6957 (tp) cc_final: 0.6714 (tp) REVERT: T 17 ILE cc_start: 0.6920 (pp) cc_final: 0.6464 (mm) REVERT: T 57 LEU cc_start: 0.6750 (mm) cc_final: 0.6483 (mm) REVERT: Y 34 ASP cc_start: 0.9249 (m-30) cc_final: 0.8986 (t0) REVERT: Y 44 GLU cc_start: 0.8664 (tp30) cc_final: 0.7747 (tp30) REVERT: Y 103 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6204 (mttt) REVERT: A 124 ASP cc_start: 0.8576 (m-30) cc_final: 0.8011 (p0) REVERT: A 228 MET cc_start: 0.8633 (mmm) cc_final: 0.8394 (mmm) REVERT: A 260 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8311 (ttp-170) REVERT: A 271 ASP cc_start: 0.8446 (t70) cc_final: 0.8093 (t0) REVERT: A 272 ASP cc_start: 0.7880 (p0) cc_final: 0.7309 (p0) REVERT: A 274 SER cc_start: 0.7824 (m) cc_final: 0.7556 (p) REVERT: A 383 LYS cc_start: 0.9100 (mttt) cc_final: 0.8866 (tppt) REVERT: A 442 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 52 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7926 (tt0) REVERT: B 62 LYS cc_start: 0.8398 (mttt) cc_final: 0.8129 (mmtt) REVERT: B 84 VAL cc_start: 0.8360 (t) cc_final: 0.8142 (p) REVERT: B 275 LYS cc_start: 0.8276 (mttm) cc_final: 0.8030 (mptt) REVERT: B 330 GLU cc_start: 0.8700 (tt0) cc_final: 0.8029 (tm-30) REVERT: B 355 GLU cc_start: 0.7984 (tt0) cc_final: 0.7060 (tp30) REVERT: B 475 LYS cc_start: 0.9247 (mttm) cc_final: 0.9007 (tptm) REVERT: C 16 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: C 146 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8077 (mp0) REVERT: C 271 ASP cc_start: 0.8147 (t0) cc_final: 0.7881 (t70) REVERT: C 272 ASP cc_start: 0.7476 (p0) cc_final: 0.7193 (p0) REVERT: C 471 LEU cc_start: 0.9170 (mt) cc_final: 0.8776 (mm) REVERT: D 38 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7896 (mm-30) REVERT: D 50 VAL cc_start: 0.7916 (t) cc_final: 0.7668 (t) REVERT: D 61 THR cc_start: 0.9166 (p) cc_final: 0.8749 (t) REVERT: D 65 ASP cc_start: 0.8303 (t70) cc_final: 0.7698 (m-30) REVERT: D 198 TYR cc_start: 0.8676 (t80) cc_final: 0.8451 (t80) REVERT: D 208 ASN cc_start: 0.7802 (t0) cc_final: 0.7577 (t0) REVERT: D 291 LEU cc_start: 0.8937 (mt) cc_final: 0.8735 (mp) REVERT: D 459 MET cc_start: 0.8256 (tpp) cc_final: 0.8048 (mmm) REVERT: E 22 ASP cc_start: 0.8279 (m-30) cc_final: 0.8044 (m-30) REVERT: E 153 ILE cc_start: 0.9487 (mp) cc_final: 0.9058 (mm) REVERT: E 208 ASN cc_start: 0.7923 (t0) cc_final: 0.7607 (t0) REVERT: E 256 ASP cc_start: 0.7229 (t70) cc_final: 0.6997 (t0) REVERT: E 262 THR cc_start: 0.8740 (m) cc_final: 0.8517 (m) REVERT: E 263 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7593 (mp10) REVERT: E 277 SER cc_start: 0.8319 (t) cc_final: 0.7683 (p) REVERT: E 319 ASP cc_start: 0.7838 (t0) cc_final: 0.7314 (t0) REVERT: E 341 GLU cc_start: 0.9454 (tt0) cc_final: 0.9100 (tm-30) REVERT: E 349 ASP cc_start: 0.8705 (t70) cc_final: 0.8097 (t0) REVERT: E 396 LEU cc_start: 0.7709 (mt) cc_final: 0.7328 (mt) REVERT: E 458 TYR cc_start: 0.8005 (t80) cc_final: 0.7435 (t80) REVERT: E 465 ASP cc_start: 0.8365 (m-30) cc_final: 0.8010 (t0) REVERT: E 467 VAL cc_start: 0.8079 (t) cc_final: 0.7767 (m) REVERT: E 472 LYS cc_start: 0.8634 (mttt) cc_final: 0.8303 (pttt) REVERT: F 56 GLU cc_start: 0.8303 (tt0) cc_final: 0.7934 (tm-30) REVERT: F 62 ILE cc_start: 0.9044 (mt) cc_final: 0.8682 (tt) REVERT: F 64 MET cc_start: 0.8504 (mmp) cc_final: 0.8164 (mmp) REVERT: F 282 GLN cc_start: 0.9212 (pm20) cc_final: 0.8521 (pm20) REVERT: F 284 THR cc_start: 0.8885 (p) cc_final: 0.8029 (t) REVERT: F 288 ASP cc_start: 0.8841 (m-30) cc_final: 0.8506 (m-30) REVERT: F 316 ASP cc_start: 0.8142 (t70) cc_final: 0.7884 (t0) REVERT: F 352 ASP cc_start: 0.8142 (t70) cc_final: 0.7812 (t0) REVERT: F 368 TYR cc_start: 0.9385 (t80) cc_final: 0.8955 (t80) REVERT: F 393 MET cc_start: 0.8321 (mtp) cc_final: 0.7005 (mmm) REVERT: F 401 LYS cc_start: 0.8277 (tttt) cc_final: 0.7685 (mttm) REVERT: F 449 TYR cc_start: 0.8919 (m-80) cc_final: 0.8646 (m-80) REVERT: F 459 MET cc_start: 0.8067 (tpp) cc_final: 0.7676 (tpp) REVERT: G 53 LYS cc_start: 0.9023 (mmpt) cc_final: 0.8659 (pttt) REVERT: G 135 LYS cc_start: 0.7007 (pttm) cc_final: 0.6467 (tppt) REVERT: G 142 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8937 (mt-10) REVERT: G 166 TYR cc_start: 0.7293 (p90) cc_final: 0.6460 (p90) REVERT: G 168 ASP cc_start: 0.7670 (t0) cc_final: 0.7204 (t0) REVERT: G 218 MET cc_start: 0.6637 (ttm) cc_final: 0.6191 (ttm) REVERT: G 246 ASP cc_start: 0.8771 (t70) cc_final: 0.8382 (t0) REVERT: H 29 GLN cc_start: 0.8486 (tt0) cc_final: 0.8280 (tp40) REVERT: H 32 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6876 (pp) REVERT: H 51 GLN cc_start: 0.7258 (pt0) cc_final: 0.6999 (pt0) REVERT: H 66 LYS cc_start: 0.7562 (mttp) cc_final: 0.7322 (mptt) REVERT: H 116 ASP cc_start: 0.8102 (m-30) cc_final: 0.7604 (p0) REVERT: H 118 ARG cc_start: 0.7089 (mmm160) cc_final: 0.6722 (mmm-85) REVERT: I 13 TYR cc_start: 0.8823 (t80) cc_final: 0.8195 (t80) REVERT: I 36 ASN cc_start: 0.8317 (m-40) cc_final: 0.7944 (t0) REVERT: I 38 SER cc_start: 0.9059 (t) cc_final: 0.8682 (p) REVERT: I 41 ASP cc_start: 0.8221 (m-30) cc_final: 0.7916 (m-30) REVERT: Z 139 GLU cc_start: 0.3482 (mm-30) cc_final: 0.2349 (tm-30) REVERT: Z 151 LYS cc_start: 0.8361 (tmtm) cc_final: 0.8113 (mmmt) REVERT: Z 195 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8710 (mm-40) REVERT: 7 24 SER cc_start: 0.4129 (p) cc_final: 0.3921 (m) REVERT: 7 42 GLN cc_start: 0.6179 (pp30) cc_final: 0.5657 (tm-30) REVERT: 7 58 TYR cc_start: 0.6218 (t80) cc_final: 0.5893 (t80) REVERT: 7 68 ILE cc_start: 0.5907 (mt) cc_final: 0.5659 (mt) REVERT: 7 107 GLU cc_start: 0.8542 (tt0) cc_final: 0.8023 (tp30) REVERT: 7 115 LYS cc_start: 0.6966 (mttt) cc_final: 0.6747 (tppt) REVERT: 7 125 GLN cc_start: 0.7236 (tp-100) cc_final: 0.7034 (mt0) REVERT: 7 173 MET cc_start: 0.5784 (pp-130) cc_final: 0.5023 (mpp) REVERT: 8 20 MET cc_start: 0.6734 (mmt) cc_final: 0.6292 (ptt) REVERT: X 46 LEU cc_start: 0.7334 (pp) cc_final: 0.6905 (mm) REVERT: X 47 THR cc_start: 0.7826 (m) cc_final: 0.6542 (m) REVERT: X 67 ASP cc_start: 0.8994 (m-30) cc_final: 0.8354 (t70) REVERT: X 69 ILE cc_start: 0.8897 (mt) cc_final: 0.8685 (tp) REVERT: X 70 MET cc_start: 0.8410 (ttt) cc_final: 0.8136 (tmm) REVERT: X 82 TRP cc_start: 0.6641 (p-90) cc_final: 0.6124 (p-90) REVERT: X 85 TYR cc_start: 0.7697 (m-80) cc_final: 0.7459 (m-80) REVERT: X 89 ILE cc_start: 0.8649 (tp) cc_final: 0.8055 (pt) REVERT: X 102 ILE cc_start: 0.8285 (mt) cc_final: 0.8066 (mm) REVERT: X 169 ARG cc_start: 0.7343 (ttm170) cc_final: 0.6773 (mtp180) REVERT: X 220 MET cc_start: 0.7428 (ttm) cc_final: 0.7131 (mmm) REVERT: X 237 LEU cc_start: 0.9332 (mp) cc_final: 0.9097 (tp) REVERT: X 246 VAL cc_start: 0.4798 (t) cc_final: 0.4549 (m) REVERT: J 1 MET cc_start: 0.2242 (ttp) cc_final: 0.1953 (tpt) REVERT: J 4 ARG cc_start: 0.5059 (ttt180) cc_final: 0.4580 (mtp85) REVERT: J 9 ILE cc_start: 0.7755 (pp) cc_final: 0.7471 (pt) outliers start: 27 outliers final: 6 residues processed: 1190 average time/residue: 0.2397 time to fit residues: 460.8439 Evaluate side-chains 623 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 614 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain H residue 32 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0030 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 2 GLN K 35 ASN R 35 ASN S 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN Y 95 ASN Y 96 ASN Y 112 ASN A 26 ASN A 145 HIS A 332 GLN A 418 GLN A 428 GLN A 432 GLN B 145 HIS B 165 GLN B 192 ASN B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN B 351 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN D 27 GLN D 221 GLN D 308 GLN D 385 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN F 52 GLN F 257 ASN F 455 HIS G 217 GLN H 44 ASN H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 GLN Z 171 GLN Z 203 GLN 7 123 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 ASN 6 38 ASN U 14 ASN X 71 ASN X 76 GLN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.124050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091148 restraints weight = 117135.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092798 restraints weight = 68779.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093019 restraints weight = 43289.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093269 restraints weight = 37788.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093513 restraints weight = 34890.739| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39481 Z= 0.155 Angle : 0.711 11.211 53507 Z= 0.358 Chirality : 0.044 0.221 6349 Planarity : 0.005 0.067 6839 Dihedral : 7.408 164.443 5489 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 10.90 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -1.63 (0.11), residues: 5060 helix: -0.65 (0.09), residues: 2699 sheet: -1.27 (0.21), residues: 581 loop : -1.46 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 486 TYR 0.019 0.002 TYR G 159 PHE 0.036 0.002 PHE 7 95 TRP 0.022 0.002 TRP X 234 HIS 0.010 0.001 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (39481) covalent geometry : angle 0.71121 / 0.36 (53507) hydrogen bonds : bond 0.04681 / 3.11 ( 2169) hydrogen bonds : angle 5.57925 / 3.92 ( 6321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 733 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: K 17 ILE cc_start: 0.2532 (OUTLIER) cc_final: 0.1886 (pp) REVERT: K 20 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5594 (mt) REVERT: K 34 ILE cc_start: 0.7011 (mt) cc_final: 0.6806 (mp) REVERT: K 53 LEU cc_start: 0.8352 (tm) cc_final: 0.7804 (mt) REVERT: K 73 LEU cc_start: 0.5288 (tp) cc_final: 0.4861 (mt) REVERT: M 46 THR cc_start: 0.7665 (m) cc_final: 0.7103 (m) REVERT: N 29 VAL cc_start: 0.8369 (t) cc_final: 0.8134 (t) REVERT: N 67 MET cc_start: 0.4792 (pp-130) cc_final: 0.4341 (ttt) REVERT: O 66 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.4973 (mt) REVERT: P 5 LEU cc_start: 0.8146 (pt) cc_final: 0.7764 (tp) REVERT: Q 10 ILE cc_start: 0.1703 (OUTLIER) cc_final: 0.1454 (tt) REVERT: R 3 LEU cc_start: 0.4304 (tt) cc_final: 0.4063 (mt) REVERT: R 4 VAL cc_start: 0.3075 (p) cc_final: 0.2576 (t) REVERT: R 19 LEU cc_start: 0.6540 (pp) cc_final: 0.5999 (mp) REVERT: R 50 MET cc_start: 0.8022 (ttt) cc_final: 0.7358 (ptm) REVERT: R 72 LEU cc_start: 0.6714 (tp) cc_final: 0.6399 (tp) REVERT: S 9 TYR cc_start: 0.7276 (m-80) cc_final: 0.7068 (m-80) REVERT: S 45 ASP cc_start: 0.8780 (m-30) cc_final: 0.8399 (t0) REVERT: S 66 LEU cc_start: 0.6949 (pt) cc_final: 0.6490 (pt) REVERT: S 70 PHE cc_start: 0.8324 (m-10) cc_final: 0.8062 (m-80) REVERT: S 72 LEU cc_start: 0.6894 (tp) cc_final: 0.6686 (tp) REVERT: Y 80 ASN cc_start: 0.6168 (OUTLIER) cc_final: 0.4801 (t0) REVERT: Y 103 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5881 (mttt) REVERT: B 30 THR cc_start: 0.7588 (t) cc_final: 0.7376 (p) REVERT: C 16 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: D 198 TYR cc_start: 0.8499 (t80) cc_final: 0.8267 (t80) REVERT: D 294 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7303 (mm-30) REVERT: D 388 ILE cc_start: 0.8582 (mt) cc_final: 0.8224 (mp) REVERT: D 409 LYS cc_start: 0.8191 (mttm) cc_final: 0.7889 (ttpt) REVERT: E 153 ILE cc_start: 0.9410 (mp) cc_final: 0.9066 (mm) REVERT: E 277 SER cc_start: 0.8603 (t) cc_final: 0.8309 (p) REVERT: E 458 TYR cc_start: 0.7527 (t80) cc_final: 0.7255 (t80) REVERT: E 465 ASP cc_start: 0.8530 (m-30) cc_final: 0.8161 (t0) REVERT: E 472 LYS cc_start: 0.8751 (mttt) cc_final: 0.8425 (pttt) REVERT: F 169 GLU cc_start: 0.7336 (tp30) cc_final: 0.7114 (tp30) REVERT: F 282 GLN cc_start: 0.8940 (pm20) cc_final: 0.8602 (pm20) REVERT: F 352 ASP cc_start: 0.7524 (t70) cc_final: 0.7178 (t0) REVERT: G 60 LEU cc_start: 0.7526 (mp) cc_final: 0.6986 (tt) REVERT: G 166 TYR cc_start: 0.8206 (p90) cc_final: 0.7426 (p90) REVERT: G 218 MET cc_start: 0.7788 (ttm) cc_final: 0.7284 (ttm) REVERT: G 250 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7850 (ttp80) REVERT: H 118 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6797 (mmm-85) REVERT: I 13 TYR cc_start: 0.8790 (t80) cc_final: 0.8172 (t80) REVERT: I 36 ASN cc_start: 0.8021 (m-40) cc_final: 0.7803 (t0) REVERT: I 44 TYR cc_start: 0.8278 (p90) cc_final: 0.7661 (p90) REVERT: Z 139 GLU cc_start: 0.3241 (mm-30) cc_final: 0.2718 (tm-30) REVERT: Z 143 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7830 (ptpp) REVERT: Z 166 GLN cc_start: 0.8125 (mm110) cc_final: 0.7626 (tm-30) REVERT: 7 83 ILE cc_start: 0.4832 (OUTLIER) cc_final: 0.4430 (pp) REVERT: 7 107 GLU cc_start: 0.8411 (tt0) cc_final: 0.7844 (tp30) REVERT: 7 151 GLU cc_start: 0.7914 (tp30) cc_final: 0.7384 (pt0) REVERT: 7 173 MET cc_start: 0.4657 (pp-130) cc_final: 0.4119 (mmt) REVERT: 6 54 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5512 (p) REVERT: 6 71 GLU cc_start: 0.3342 (mp0) cc_final: 0.2756 (pt0) REVERT: U 9 VAL cc_start: 0.4596 (OUTLIER) cc_final: 0.4355 (p) REVERT: 8 10 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6613 (mmm) REVERT: 8 36 LEU cc_start: 0.6167 (mt) cc_final: 0.5863 (mt) REVERT: X 46 LEU cc_start: 0.7529 (pp) cc_final: 0.6783 (mm) REVERT: X 47 THR cc_start: 0.7536 (m) cc_final: 0.6158 (m) REVERT: X 57 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7548 (mtm-85) REVERT: X 58 TRP cc_start: 0.7697 (t-100) cc_final: 0.7282 (t-100) REVERT: X 70 MET cc_start: 0.8091 (ttt) cc_final: 0.7796 (tmm) REVERT: X 84 LEU cc_start: 0.8130 (tt) cc_final: 0.7879 (mt) REVERT: X 89 ILE cc_start: 0.8542 (tp) cc_final: 0.8203 (pt) REVERT: X 122 SER cc_start: 0.7916 (t) cc_final: 0.7603 (p) REVERT: X 166 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: X 169 ARG cc_start: 0.6912 (ttm170) cc_final: 0.6073 (mtp180) REVERT: X 222 LEU cc_start: 0.7773 (tt) cc_final: 0.7565 (mt) outliers start: 108 outliers final: 47 residues processed: 796 average time/residue: 0.2276 time to fit residues: 300.5752 Evaluate side-chains 582 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 523 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain Y residue 59 ASN Chi-restraints excluded: chain Y residue 80 ASN Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 38 LEU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 166 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 14 optimal weight: 20.0000 chunk 435 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 365 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 384 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 227 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 85 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 35 ASN P 2 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 ASN A 26 ASN B 145 HIS ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN H 44 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN 7 125 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.122081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089011 restraints weight = 117567.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091394 restraints weight = 62698.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091551 restraints weight = 37097.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092017 restraints weight = 32549.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092214 restraints weight = 29717.003| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39481 Z= 0.133 Angle : 0.666 12.750 53507 Z= 0.332 Chirality : 0.044 0.278 6349 Planarity : 0.004 0.064 6839 Dihedral : 6.925 163.041 5485 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 2.37 % Allowed : 13.39 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.91 (0.12), residues: 5060 helix: 0.06 (0.10), residues: 2693 sheet: -1.01 (0.21), residues: 592 loop : -1.33 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 260 TYR 0.023 0.001 TYR E 368 PHE 0.020 0.002 PHE R 48 TRP 0.037 0.002 TRP X 234 HIS 0.007 0.001 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (39481) covalent geometry : angle 0.66569 / 0.33 (53507) hydrogen bonds : bond 0.04041 / 2.70 ( 2169) hydrogen bonds : angle 5.13152 / 3.62 ( 6321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 597 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.5818 (tmm) REVERT: M 44 LYS cc_start: 0.7791 (tptt) cc_final: 0.7526 (ttmm) REVERT: M 50 MET cc_start: 0.7274 (tpp) cc_final: 0.7058 (tpp) REVERT: N 67 MET cc_start: 0.4740 (pp-130) cc_final: 0.4306 (ttt) REVERT: O 66 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5431 (mt) REVERT: P 5 LEU cc_start: 0.8142 (pt) cc_final: 0.7763 (tp) REVERT: Q 10 ILE cc_start: 0.1791 (OUTLIER) cc_final: 0.1546 (tt) REVERT: R 4 VAL cc_start: 0.3526 (p) cc_final: 0.3009 (t) REVERT: S 45 ASP cc_start: 0.8724 (m-30) cc_final: 0.8299 (t0) REVERT: S 66 LEU cc_start: 0.6946 (pt) cc_final: 0.6696 (pt) REVERT: S 67 MET cc_start: 0.7746 (tpt) cc_final: 0.7359 (tpp) REVERT: S 72 LEU cc_start: 0.7333 (tp) cc_final: 0.6987 (tp) REVERT: T 67 MET cc_start: 0.7983 (tmm) cc_final: 0.7577 (ptt) REVERT: Y 34 ASP cc_start: 0.8485 (t0) cc_final: 0.8225 (t0) REVERT: Y 103 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5669 (mttt) REVERT: Y 123 VAL cc_start: 0.8452 (m) cc_final: 0.8227 (t) REVERT: C 15 GLU cc_start: 0.7676 (pt0) cc_final: 0.7466 (pt0) REVERT: C 16 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: D 84 SER cc_start: 0.8238 (m) cc_final: 0.7887 (t) REVERT: D 198 TYR cc_start: 0.8515 (t80) cc_final: 0.8278 (t80) REVERT: D 294 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7400 (mm-30) REVERT: D 409 LYS cc_start: 0.8273 (mttm) cc_final: 0.7890 (ttpt) REVERT: E 22 ASP cc_start: 0.7662 (m-30) cc_final: 0.7404 (m-30) REVERT: E 153 ILE cc_start: 0.9335 (mp) cc_final: 0.9012 (mm) REVERT: E 277 SER cc_start: 0.8763 (t) cc_final: 0.8386 (p) REVERT: E 306 SER cc_start: 0.9188 (t) cc_final: 0.8864 (p) REVERT: E 465 ASP cc_start: 0.8484 (m-30) cc_final: 0.8009 (t0) REVERT: E 472 LYS cc_start: 0.8734 (mttt) cc_final: 0.8411 (pttt) REVERT: F 201 MET cc_start: 0.8192 (mmp) cc_final: 0.7973 (mmm) REVERT: F 282 GLN cc_start: 0.8983 (pm20) cc_final: 0.8592 (pm20) REVERT: F 341 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7353 (tm-30) REVERT: G 10 LEU cc_start: 0.9114 (tp) cc_final: 0.8862 (tp) REVERT: G 23 MET cc_start: 0.8215 (ttm) cc_final: 0.7963 (ttm) REVERT: G 166 TYR cc_start: 0.8048 (p90) cc_final: 0.7072 (p90) REVERT: G 218 MET cc_start: 0.7746 (ttm) cc_final: 0.7401 (ttm) REVERT: G 266 GLU cc_start: 0.7805 (pp20) cc_final: 0.7572 (pp20) REVERT: H 118 ARG cc_start: 0.6863 (mmm160) cc_final: 0.6652 (mmm-85) REVERT: H 133 LEU cc_start: 0.7901 (mt) cc_final: 0.7350 (tp) REVERT: I 13 TYR cc_start: 0.8780 (t80) cc_final: 0.8205 (t80) REVERT: I 36 ASN cc_start: 0.8072 (m-40) cc_final: 0.7872 (t0) REVERT: I 44 TYR cc_start: 0.8237 (p90) cc_final: 0.7575 (p90) REVERT: Z 129 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: Z 139 GLU cc_start: 0.3160 (mm-30) cc_final: 0.2886 (tm-30) REVERT: Z 157 TRP cc_start: 0.6266 (m100) cc_final: 0.5978 (m100) REVERT: 7 45 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8248 (pt0) REVERT: 7 83 ILE cc_start: 0.4990 (OUTLIER) cc_final: 0.4518 (pp) REVERT: 7 95 PHE cc_start: 0.6978 (m-80) cc_final: 0.6734 (m-80) REVERT: 7 107 GLU cc_start: 0.8494 (tt0) cc_final: 0.7933 (tp30) REVERT: 7 151 GLU cc_start: 0.7789 (tp30) cc_final: 0.7254 (pt0) REVERT: 6 7 TYR cc_start: 0.7515 (t80) cc_final: 0.7165 (t80) REVERT: 6 54 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.5530 (p) REVERT: U 9 VAL cc_start: 0.4509 (OUTLIER) cc_final: 0.4205 (p) REVERT: 8 10 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.5951 (tmm) REVERT: X 30 SER cc_start: 0.2525 (OUTLIER) cc_final: 0.2252 (m) REVERT: X 46 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6874 (mt) REVERT: X 47 THR cc_start: 0.7240 (m) cc_final: 0.6065 (m) REVERT: X 57 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7529 (mtm-85) REVERT: X 58 TRP cc_start: 0.7794 (t-100) cc_final: 0.7190 (t-100) REVERT: X 89 ILE cc_start: 0.8491 (tp) cc_final: 0.8170 (pt) REVERT: X 94 MET cc_start: 0.7351 (tpp) cc_final: 0.6172 (mmm) REVERT: X 104 MET cc_start: 0.4357 (ptt) cc_final: 0.4054 (ttp) REVERT: X 166 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: X 169 ARG cc_start: 0.6996 (ttm170) cc_final: 0.6421 (mtp180) REVERT: X 220 MET cc_start: 0.7358 (mmp) cc_final: 0.6729 (mmp) REVERT: J 1 MET cc_start: 0.2439 (tmm) cc_final: 0.0862 (tpt) REVERT: J 3 LYS cc_start: 0.6682 (mmtm) cc_final: 0.6423 (tmtt) outliers start: 97 outliers final: 42 residues processed: 660 average time/residue: 0.2155 time to fit residues: 241.0808 Evaluate side-chains 552 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 497 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 401 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 30 SER Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 166 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 367 optimal weight: 0.3980 chunk 481 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 314 optimal weight: 0.0980 chunk 404 optimal weight: 6.9990 chunk 239 optimal weight: 0.5980 chunk 461 optimal weight: 0.4980 chunk 371 optimal weight: 2.9990 chunk 448 optimal weight: 5.9990 chunk 472 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 35 ASN N 2 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 187 ASN D 308 GLN E 24 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 GLN 7 98 HIS 7 123 ASN 6 22 GLN 8 11 ASN X 62 GLN X 230 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089527 restraints weight = 117478.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091728 restraints weight = 64594.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092096 restraints weight = 43091.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092538 restraints weight = 33962.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092750 restraints weight = 30903.908| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39481 Z= 0.130 Angle : 0.645 13.727 53507 Z= 0.318 Chirality : 0.043 0.216 6349 Planarity : 0.004 0.059 6839 Dihedral : 6.615 161.262 5481 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 2.76 % Allowed : 13.88 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.47 (0.12), residues: 5060 helix: 0.45 (0.10), residues: 2704 sheet: -0.92 (0.21), residues: 612 loop : -1.14 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 250 TYR 0.032 0.002 TYR S 9 PHE 0.034 0.001 PHE S 64 TRP 0.032 0.002 TRP X 234 HIS 0.006 0.001 HIS 6 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (39481) covalent geometry : angle 0.64530 / 0.32 (53507) hydrogen bonds : bond 0.03728 / 2.49 ( 2169) hydrogen bonds : angle 4.91366 / 3.46 ( 6321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 564 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5749 (tmm) REVERT: M 44 LYS cc_start: 0.7938 (tptt) cc_final: 0.7713 (ttmm) REVERT: N 67 MET cc_start: 0.4689 (pp-130) cc_final: 0.4366 (ttt) REVERT: O 66 LEU cc_start: 0.5814 (OUTLIER) cc_final: 0.5514 (mt) REVERT: P 5 LEU cc_start: 0.8135 (pt) cc_final: 0.7754 (tp) REVERT: P 53 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6904 (mp) REVERT: Q 37 VAL cc_start: 0.9381 (m) cc_final: 0.9177 (p) REVERT: R 4 VAL cc_start: 0.3014 (p) cc_final: 0.2783 (t) REVERT: S 8 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7605 (ttmt) REVERT: S 48 PHE cc_start: 0.7980 (t80) cc_final: 0.7700 (t80) REVERT: S 67 MET cc_start: 0.7788 (tpt) cc_final: 0.7467 (tpp) REVERT: S 70 PHE cc_start: 0.8182 (m-80) cc_final: 0.7710 (m-80) REVERT: S 72 LEU cc_start: 0.7224 (tp) cc_final: 0.6670 (tp) REVERT: T 9 TYR cc_start: 0.7742 (m-80) cc_final: 0.7464 (m-10) REVERT: T 67 MET cc_start: 0.7943 (tmm) cc_final: 0.7605 (ptt) REVERT: Y 103 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5908 (mttt) REVERT: Y 123 VAL cc_start: 0.8450 (m) cc_final: 0.8159 (t) REVERT: C 11 SER cc_start: 0.8766 (m) cc_final: 0.8269 (t) REVERT: C 15 GLU cc_start: 0.7740 (pt0) cc_final: 0.7489 (pt0) REVERT: D 64 MET cc_start: 0.8349 (mmm) cc_final: 0.8082 (mmm) REVERT: D 84 SER cc_start: 0.8339 (m) cc_final: 0.8072 (t) REVERT: D 198 TYR cc_start: 0.8499 (t80) cc_final: 0.8247 (t80) REVERT: D 294 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7445 (mm-30) REVERT: D 409 LYS cc_start: 0.8321 (mttm) cc_final: 0.8010 (ttpt) REVERT: D 459 MET cc_start: 0.7795 (mmp) cc_final: 0.7479 (mmm) REVERT: E 277 SER cc_start: 0.8846 (t) cc_final: 0.8293 (p) REVERT: E 306 SER cc_start: 0.9071 (t) cc_final: 0.8568 (p) REVERT: E 458 TYR cc_start: 0.7498 (t80) cc_final: 0.7150 (t80) REVERT: E 465 ASP cc_start: 0.8475 (m-30) cc_final: 0.7989 (t0) REVERT: E 472 LYS cc_start: 0.8738 (mttt) cc_final: 0.8414 (pttt) REVERT: F 282 GLN cc_start: 0.9020 (pm20) cc_final: 0.8754 (pm20) REVERT: G 10 LEU cc_start: 0.9139 (tp) cc_final: 0.8871 (tp) REVERT: G 23 MET cc_start: 0.8206 (ttm) cc_final: 0.7866 (ttm) REVERT: G 52 TYR cc_start: 0.7289 (m-80) cc_final: 0.6763 (m-10) REVERT: G 166 TYR cc_start: 0.8174 (p90) cc_final: 0.7235 (p90) REVERT: G 218 MET cc_start: 0.7749 (ttm) cc_final: 0.7529 (ttm) REVERT: G 247 MET cc_start: 0.8334 (mmm) cc_final: 0.8010 (mmm) REVERT: G 266 GLU cc_start: 0.7843 (pp20) cc_final: 0.7616 (pp20) REVERT: H 35 LYS cc_start: 0.8672 (tttt) cc_final: 0.8231 (ttpt) REVERT: H 109 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8842 (mmmt) REVERT: H 133 LEU cc_start: 0.7891 (mt) cc_final: 0.7620 (tp) REVERT: I 13 TYR cc_start: 0.8800 (t80) cc_final: 0.8177 (t80) REVERT: I 29 LEU cc_start: 0.7355 (mt) cc_final: 0.7119 (pp) REVERT: I 44 TYR cc_start: 0.8273 (p90) cc_final: 0.7546 (p90) REVERT: Z 129 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: Z 157 TRP cc_start: 0.6396 (m100) cc_final: 0.6138 (m100) REVERT: Z 170 ARG cc_start: 0.7640 (tmm160) cc_final: 0.6861 (tmm-80) REVERT: 7 83 ILE cc_start: 0.4946 (OUTLIER) cc_final: 0.4520 (pp) REVERT: 7 107 GLU cc_start: 0.8507 (tt0) cc_final: 0.7953 (tp30) REVERT: 7 151 GLU cc_start: 0.7829 (tp30) cc_final: 0.7337 (pt0) REVERT: 6 54 THR cc_start: 0.5762 (OUTLIER) cc_final: 0.5555 (p) REVERT: 6 71 GLU cc_start: 0.3684 (mp0) cc_final: 0.3342 (pt0) REVERT: 8 10 MET cc_start: 0.7023 (mmt) cc_final: 0.6014 (tmm) REVERT: 8 11 ASN cc_start: 0.7385 (t160) cc_final: 0.7152 (t0) REVERT: X 46 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6941 (mm) REVERT: X 47 THR cc_start: 0.7236 (m) cc_final: 0.6005 (m) REVERT: X 57 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7881 (mtm-85) REVERT: X 58 TRP cc_start: 0.7911 (t-100) cc_final: 0.7341 (t-100) REVERT: X 89 ILE cc_start: 0.8468 (tp) cc_final: 0.8030 (pt) REVERT: X 94 MET cc_start: 0.7463 (tpp) cc_final: 0.6585 (mmm) REVERT: X 104 MET cc_start: 0.4493 (ptt) cc_final: 0.4147 (tmm) REVERT: X 166 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: X 169 ARG cc_start: 0.6891 (ttm170) cc_final: 0.6431 (mtp180) REVERT: X 220 MET cc_start: 0.7741 (mmp) cc_final: 0.7199 (mmp) REVERT: J 1 MET cc_start: 0.3029 (tmm) cc_final: 0.1766 (tmm) outliers start: 113 outliers final: 62 residues processed: 639 average time/residue: 0.2097 time to fit residues: 227.3399 Evaluate side-chains 565 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 494 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 103 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 25 THR Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 126 SER Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain 8 residue 13 LEU Chi-restraints excluded: chain 8 residue 19 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 166 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 355 optimal weight: 0.8980 chunk 479 optimal weight: 0.0570 chunk 493 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 469 optimal weight: 50.0000 chunk 422 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 362 optimal weight: 0.0270 overall best weight: 1.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 ASN Y 188 ASN A 48 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 GLN E 195 ASN F 249 GLN H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.121918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088880 restraints weight = 116471.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090528 restraints weight = 66762.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091711 restraints weight = 40265.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091423 restraints weight = 36931.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.091445 restraints weight = 30967.573| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39481 Z= 0.157 Angle : 0.653 13.159 53507 Z= 0.322 Chirality : 0.043 0.223 6349 Planarity : 0.004 0.062 6839 Dihedral : 6.430 160.300 5478 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 3.08 % Allowed : 14.47 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.19 (0.12), residues: 5060 helix: 0.68 (0.10), residues: 2701 sheet: -0.87 (0.21), residues: 614 loop : -0.99 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 250 TYR 0.019 0.001 TYR G 52 PHE 0.036 0.002 PHE S 64 TRP 0.035 0.002 TRP X 234 HIS 0.006 0.001 HIS X 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (39481) covalent geometry : angle 0.65343 / 0.32 (53507) hydrogen bonds : bond 0.03637 / 2.42 ( 2169) hydrogen bonds : angle 4.81994 / 3.40 ( 6321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 544 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7151 (tp) cc_final: 0.6828 (mt) REVERT: L 67 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5810 (tmm) REVERT: M 50 MET cc_start: 0.7702 (tpp) cc_final: 0.7473 (tpp) REVERT: N 66 LEU cc_start: 0.2880 (OUTLIER) cc_final: 0.2266 (tt) REVERT: N 67 MET cc_start: 0.4840 (pp-130) cc_final: 0.4186 (ttt) REVERT: N 70 PHE cc_start: 0.6470 (m-10) cc_final: 0.5305 (t80) REVERT: O 66 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5669 (mt) REVERT: S 67 MET cc_start: 0.7846 (tpt) cc_final: 0.7479 (tpp) REVERT: S 70 PHE cc_start: 0.8315 (m-80) cc_final: 0.7605 (m-80) REVERT: T 67 MET cc_start: 0.7957 (tmm) cc_final: 0.7609 (ptt) REVERT: Y 34 ASP cc_start: 0.8091 (t0) cc_final: 0.7853 (t0) REVERT: Y 123 VAL cc_start: 0.8433 (m) cc_final: 0.8047 (t) REVERT: A 303 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8943 (tp) REVERT: A 484 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8212 (tp30) REVERT: C 11 SER cc_start: 0.8697 (m) cc_final: 0.8234 (t) REVERT: C 15 GLU cc_start: 0.7853 (pt0) cc_final: 0.7587 (pt0) REVERT: D 84 SER cc_start: 0.8275 (m) cc_final: 0.8006 (p) REVERT: D 294 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7419 (mm-30) REVERT: E 267 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7214 (mt-10) REVERT: E 402 LEU cc_start: 0.9002 (tp) cc_final: 0.8553 (pp) REVERT: E 458 TYR cc_start: 0.7351 (t80) cc_final: 0.7109 (t80) REVERT: E 465 ASP cc_start: 0.8473 (m-30) cc_final: 0.7995 (t0) REVERT: E 472 LYS cc_start: 0.8749 (mttt) cc_final: 0.8426 (pttt) REVERT: F 414 LEU cc_start: 0.8799 (mt) cc_final: 0.8492 (mt) REVERT: G 10 LEU cc_start: 0.9238 (tp) cc_final: 0.8840 (tp) REVERT: G 23 MET cc_start: 0.8030 (ttm) cc_final: 0.7696 (ttm) REVERT: G 52 TYR cc_start: 0.7265 (m-80) cc_final: 0.6958 (m-10) REVERT: G 60 LEU cc_start: 0.7477 (mp) cc_final: 0.7124 (mp) REVERT: G 166 TYR cc_start: 0.8217 (p90) cc_final: 0.7274 (p90) REVERT: G 266 GLU cc_start: 0.7786 (pp20) cc_final: 0.7581 (pp20) REVERT: H 96 PHE cc_start: 0.3752 (t80) cc_final: 0.3511 (t80) REVERT: H 109 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8745 (mmmt) REVERT: H 133 LEU cc_start: 0.8098 (mt) cc_final: 0.7722 (tp) REVERT: I 13 TYR cc_start: 0.8842 (t80) cc_final: 0.8290 (t80) REVERT: Z 129 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: Z 140 LEU cc_start: 0.7275 (tp) cc_final: 0.7038 (mm) REVERT: Z 157 TRP cc_start: 0.6397 (m100) cc_final: 0.6097 (m100) REVERT: Z 159 ARG cc_start: 0.7689 (tmm160) cc_final: 0.6930 (ptt180) REVERT: Z 160 TYR cc_start: 0.6988 (t80) cc_final: 0.6334 (t80) REVERT: Z 170 ARG cc_start: 0.7747 (tmm160) cc_final: 0.6977 (tmm-80) REVERT: 7 95 PHE cc_start: 0.7173 (m-80) cc_final: 0.6913 (m-80) REVERT: 7 96 GLU cc_start: 0.7659 (pp20) cc_final: 0.7433 (pt0) REVERT: 7 105 GLU cc_start: 0.6405 (tt0) cc_final: 0.5607 (pt0) REVERT: 7 151 GLU cc_start: 0.7930 (tp30) cc_final: 0.7350 (pt0) REVERT: 7 163 TYR cc_start: 0.6277 (t80) cc_final: 0.5979 (t80) REVERT: 8 10 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6101 (tmm) REVERT: 8 11 ASN cc_start: 0.7363 (t160) cc_final: 0.7133 (t0) REVERT: X 46 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7130 (mm) REVERT: X 47 THR cc_start: 0.7340 (m) cc_final: 0.5842 (m) REVERT: X 57 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7786 (mtm-85) REVERT: X 58 TRP cc_start: 0.7887 (t-100) cc_final: 0.7187 (t-100) REVERT: X 104 MET cc_start: 0.4380 (ptt) cc_final: 0.3948 (tmm) REVERT: X 220 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7557 (mmp) REVERT: J 1 MET cc_start: 0.2574 (tmm) cc_final: 0.1596 (tmm) outliers start: 126 outliers final: 78 residues processed: 617 average time/residue: 0.2114 time to fit residues: 221.7626 Evaluate side-chains 560 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 474 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 25 THR Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 138 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain X residue 220 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 347 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 403 optimal weight: 0.9980 chunk 490 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 492 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 407 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS B 174 GLN B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS F 328 HIS ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.121205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086819 restraints weight = 116858.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088830 restraints weight = 60527.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.090106 restraints weight = 38863.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090921 restraints weight = 29178.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091411 restraints weight = 24322.353| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39481 Z= 0.126 Angle : 0.639 13.644 53507 Z= 0.312 Chirality : 0.043 0.225 6349 Planarity : 0.004 0.061 6839 Dihedral : 6.277 160.636 5474 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 2.69 % Allowed : 15.93 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 5060 helix: 0.87 (0.10), residues: 2710 sheet: -0.71 (0.21), residues: 591 loop : -0.89 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 250 TYR 0.024 0.001 TYR F 458 PHE 0.038 0.002 PHE S 64 TRP 0.033 0.002 TRP X 234 HIS 0.006 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (39481) covalent geometry : angle 0.63936 / 0.31 (53507) hydrogen bonds : bond 0.03484 / 2.32 ( 2169) hydrogen bonds : angle 4.68465 / 3.31 ( 6321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 527 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7432 (tp) cc_final: 0.7159 (mt) REVERT: K 48 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: M 50 MET cc_start: 0.7388 (tpp) cc_final: 0.7041 (tpp) REVERT: N 66 LEU cc_start: 0.3100 (OUTLIER) cc_final: 0.2604 (tt) REVERT: N 67 MET cc_start: 0.4740 (pp-130) cc_final: 0.4167 (ttt) REVERT: N 70 PHE cc_start: 0.6269 (m-10) cc_final: 0.5318 (t80) REVERT: O 66 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5228 (mt) REVERT: P 53 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6988 (mp) REVERT: S 67 MET cc_start: 0.7836 (tpt) cc_final: 0.7473 (tpp) REVERT: S 70 PHE cc_start: 0.7939 (m-80) cc_final: 0.7527 (m-80) REVERT: Y 34 ASP cc_start: 0.7879 (t0) cc_final: 0.7639 (t0) REVERT: Y 123 VAL cc_start: 0.8237 (m) cc_final: 0.7913 (t) REVERT: A 303 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8868 (tp) REVERT: A 484 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8167 (tp30) REVERT: C 11 SER cc_start: 0.8735 (m) cc_final: 0.8257 (t) REVERT: C 15 GLU cc_start: 0.7797 (pt0) cc_final: 0.7531 (pt0) REVERT: D 64 MET cc_start: 0.8117 (mmm) cc_final: 0.7706 (mmp) REVERT: E 22 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6898 (t0) REVERT: E 465 ASP cc_start: 0.8249 (m-30) cc_final: 0.7903 (t0) REVERT: E 472 LYS cc_start: 0.8661 (mttt) cc_final: 0.8437 (pttt) REVERT: F 169 GLU cc_start: 0.6764 (tp30) cc_final: 0.5781 (tp30) REVERT: F 459 MET cc_start: 0.7883 (tpp) cc_final: 0.7647 (tpp) REVERT: G 10 LEU cc_start: 0.9235 (tp) cc_final: 0.8960 (tp) REVERT: G 23 MET cc_start: 0.8067 (ttm) cc_final: 0.7787 (ttm) REVERT: G 52 TYR cc_start: 0.7152 (m-80) cc_final: 0.6933 (m-10) REVERT: G 145 LEU cc_start: 0.8443 (mt) cc_final: 0.8237 (mt) REVERT: G 166 TYR cc_start: 0.8026 (p90) cc_final: 0.7224 (p90) REVERT: H 60 MET cc_start: 0.6547 (mpp) cc_final: 0.6117 (mpp) REVERT: H 109 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8659 (mmmt) REVERT: I 13 TYR cc_start: 0.8657 (t80) cc_final: 0.8107 (t80) REVERT: Z 129 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: Z 139 GLU cc_start: 0.6335 (tm-30) cc_final: 0.6022 (tm-30) REVERT: Z 140 LEU cc_start: 0.7329 (tp) cc_final: 0.6981 (mm) REVERT: Z 159 ARG cc_start: 0.7641 (tmm160) cc_final: 0.6978 (ptt180) REVERT: Z 160 TYR cc_start: 0.6965 (t80) cc_final: 0.6434 (t80) REVERT: Z 170 ARG cc_start: 0.7659 (tmm160) cc_final: 0.6905 (tmm-80) REVERT: 7 95 PHE cc_start: 0.6878 (m-80) cc_final: 0.6582 (m-80) REVERT: 7 163 TYR cc_start: 0.6154 (t80) cc_final: 0.5447 (t80) REVERT: 8 10 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.5998 (tmm) REVERT: 8 11 ASN cc_start: 0.7167 (t160) cc_final: 0.6872 (t0) REVERT: X 46 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6937 (mm) REVERT: X 47 THR cc_start: 0.7345 (m) cc_final: 0.5972 (m) REVERT: X 57 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7781 (mtm-85) REVERT: X 58 TRP cc_start: 0.7933 (t-100) cc_final: 0.7108 (t-100) REVERT: X 89 ILE cc_start: 0.8288 (tp) cc_final: 0.7862 (pt) REVERT: X 93 PHE cc_start: 0.7359 (t80) cc_final: 0.7119 (t80) REVERT: X 94 MET cc_start: 0.7392 (tpp) cc_final: 0.6587 (mmm) REVERT: X 104 MET cc_start: 0.4441 (ptt) cc_final: 0.4020 (tmm) REVERT: X 169 ARG cc_start: 0.7905 (tmm-80) cc_final: 0.6969 (ttt180) REVERT: X 220 MET cc_start: 0.7866 (mmp) cc_final: 0.7556 (mmp) REVERT: J 1 MET cc_start: 0.2451 (tmm) cc_final: 0.1361 (tmm) REVERT: J 25 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4867 (m-80) outliers start: 110 outliers final: 72 residues processed: 592 average time/residue: 0.2084 time to fit residues: 210.8559 Evaluate side-chains 556 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 474 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 PHE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 44 LYS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 25 THR Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 59 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain J residue 25 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 122 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS E 127 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 GLN Z 203 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.121384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086417 restraints weight = 116255.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088427 restraints weight = 60656.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089736 restraints weight = 39191.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090527 restraints weight = 29300.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091031 restraints weight = 24610.677| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39481 Z= 0.153 Angle : 0.652 15.307 53507 Z= 0.319 Chirality : 0.043 0.227 6349 Planarity : 0.004 0.064 6839 Dihedral : 6.211 164.446 5471 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 3.05 % Allowed : 16.20 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: 0.18 (0.12), residues: 5060 helix: 0.94 (0.10), residues: 2725 sheet: -0.69 (0.21), residues: 603 loop : -0.79 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 250 TYR 0.019 0.001 TYR F 458 PHE 0.035 0.002 PHE S 64 TRP 0.037 0.002 TRP X 234 HIS 0.007 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (39481) covalent geometry : angle 0.65220 / 0.32 (53507) hydrogen bonds : bond 0.03486 / 2.33 ( 2169) hydrogen bonds : angle 4.65963 / 3.29 ( 6321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 494 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7467 (tp) cc_final: 0.6997 (mt) REVERT: K 30 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6458 (m-10) REVERT: K 48 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: M 30 PHE cc_start: 0.7639 (m-80) cc_final: 0.7148 (m-10) REVERT: M 44 LYS cc_start: 0.8285 (pttt) cc_final: 0.8046 (ptmt) REVERT: M 50 MET cc_start: 0.7623 (tpp) cc_final: 0.7303 (tpp) REVERT: N 66 LEU cc_start: 0.3414 (OUTLIER) cc_final: 0.2977 (tt) REVERT: N 67 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4309 (ttt) REVERT: N 70 PHE cc_start: 0.6203 (m-10) cc_final: 0.5351 (t80) REVERT: O 66 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5442 (mt) REVERT: P 53 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7001 (mp) REVERT: P 67 MET cc_start: 0.5193 (ppp) cc_final: 0.4337 (mtp) REVERT: S 67 MET cc_start: 0.7832 (tpt) cc_final: 0.7457 (tpp) REVERT: S 70 PHE cc_start: 0.8024 (m-80) cc_final: 0.7597 (m-80) REVERT: Y 34 ASP cc_start: 0.8019 (t0) cc_final: 0.7750 (t0) REVERT: Y 184 ILE cc_start: 0.7314 (mt) cc_final: 0.7095 (mt) REVERT: A 303 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8927 (tp) REVERT: B 281 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8195 (ptt-90) REVERT: C 11 SER cc_start: 0.8755 (m) cc_final: 0.8417 (t) REVERT: C 15 GLU cc_start: 0.7788 (pt0) cc_final: 0.7542 (pt0) REVERT: D 198 TYR cc_start: 0.8462 (t80) cc_final: 0.8167 (t80) REVERT: E 22 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6921 (t0) REVERT: E 267 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7161 (mt-10) REVERT: E 465 ASP cc_start: 0.8296 (m-30) cc_final: 0.7950 (t0) REVERT: F 414 LEU cc_start: 0.8846 (mt) cc_final: 0.8557 (mt) REVERT: F 459 MET cc_start: 0.7936 (tpp) cc_final: 0.7682 (tpp) REVERT: G 10 LEU cc_start: 0.9186 (tp) cc_final: 0.8816 (tp) REVERT: G 60 LEU cc_start: 0.7390 (mp) cc_final: 0.7154 (mp) REVERT: G 140 PHE cc_start: 0.8100 (t80) cc_final: 0.7805 (t80) REVERT: G 145 LEU cc_start: 0.8466 (mt) cc_final: 0.8236 (mt) REVERT: G 166 TYR cc_start: 0.7961 (p90) cc_final: 0.7089 (p90) REVERT: H 60 MET cc_start: 0.6780 (mpp) cc_final: 0.6519 (mpp) REVERT: H 83 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7582 (tt) REVERT: H 109 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8665 (mmmt) REVERT: I 13 TYR cc_start: 0.8723 (t80) cc_final: 0.8166 (t80) REVERT: Z 129 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: Z 139 GLU cc_start: 0.6298 (tm-30) cc_final: 0.5932 (tm-30) REVERT: Z 140 LEU cc_start: 0.7345 (tp) cc_final: 0.7002 (mm) REVERT: Z 157 TRP cc_start: 0.6467 (m100) cc_final: 0.6149 (m100) REVERT: Z 159 ARG cc_start: 0.7481 (tmm160) cc_final: 0.6939 (ptt180) REVERT: Z 160 TYR cc_start: 0.6984 (t80) cc_final: 0.6463 (t80) REVERT: Z 170 ARG cc_start: 0.7524 (tmm160) cc_final: 0.6731 (tmm-80) REVERT: 7 95 PHE cc_start: 0.6607 (m-80) cc_final: 0.6402 (m-80) REVERT: 7 163 TYR cc_start: 0.6071 (t80) cc_final: 0.5351 (t80) REVERT: 8 10 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.5884 (tmm) REVERT: X 46 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7216 (mm) REVERT: X 47 THR cc_start: 0.7426 (m) cc_final: 0.6047 (m) REVERT: X 57 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: X 58 TRP cc_start: 0.7962 (t-100) cc_final: 0.7116 (t-100) REVERT: X 94 MET cc_start: 0.7584 (tpp) cc_final: 0.6535 (mmm) REVERT: X 104 MET cc_start: 0.4526 (ptt) cc_final: 0.4059 (tmm) REVERT: X 169 ARG cc_start: 0.7853 (tmm-80) cc_final: 0.6844 (ttt180) REVERT: J 1 MET cc_start: 0.2137 (tmm) cc_final: 0.1411 (tmm) REVERT: J 25 TYR cc_start: 0.5178 (OUTLIER) cc_final: 0.4800 (m-80) outliers start: 125 outliers final: 88 residues processed: 571 average time/residue: 0.2083 time to fit residues: 201.8034 Evaluate side-chains 549 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 447 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 PHE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 13 PHE Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain 7 residue 25 THR Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 59 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain J residue 25 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 381 optimal weight: 1.9990 chunk 393 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 454 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 462 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 GLN 7 98 HIS X 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.120412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085893 restraints weight = 115775.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088245 restraints weight = 64378.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088877 restraints weight = 36210.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089058 restraints weight = 29931.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089292 restraints weight = 29936.292| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39481 Z= 0.137 Angle : 0.657 14.509 53507 Z= 0.320 Chirality : 0.043 0.264 6349 Planarity : 0.004 0.064 6839 Dihedral : 6.290 179.544 5471 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.93 % Allowed : 16.37 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: 0.29 (0.12), residues: 5060 helix: 1.02 (0.10), residues: 2727 sheet: -0.56 (0.21), residues: 595 loop : -0.75 (0.16), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 250 TYR 0.027 0.001 TYR 7 58 PHE 0.037 0.002 PHE S 64 TRP 0.035 0.002 TRP X 234 HIS 0.007 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (39481) covalent geometry : angle 0.65659 / 0.32 (53507) hydrogen bonds : bond 0.03434 / 2.29 ( 2169) hydrogen bonds : angle 4.61387 / 3.25 ( 6321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 487 time to evaluate : 1.450 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: K 20 LEU cc_start: 0.7454 (tp) cc_final: 0.6999 (mt) REVERT: K 30 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: K 35 ASN cc_start: 0.8763 (m-40) cc_final: 0.8546 (m-40) REVERT: K 48 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: L 67 MET cc_start: 0.7852 (tmm) cc_final: 0.7053 (tmm) REVERT: M 30 PHE cc_start: 0.7690 (m-80) cc_final: 0.7151 (m-10) REVERT: M 44 LYS cc_start: 0.8190 (pttt) cc_final: 0.7971 (ptmt) REVERT: M 50 MET cc_start: 0.7748 (tpp) cc_final: 0.7389 (tpp) REVERT: N 66 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3741 (tt) REVERT: N 67 MET cc_start: 0.4855 (OUTLIER) cc_final: 0.4304 (ttt) REVERT: N 70 PHE cc_start: 0.6455 (m-10) cc_final: 0.5175 (t80) REVERT: O 19 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4775 (tt) REVERT: O 66 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5254 (mt) REVERT: P 53 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6973 (mp) REVERT: S 67 MET cc_start: 0.7856 (tpt) cc_final: 0.7461 (tpp) REVERT: S 70 PHE cc_start: 0.8140 (m-80) cc_final: 0.7605 (m-80) REVERT: Y 34 ASP cc_start: 0.8367 (t0) cc_final: 0.8077 (t0) REVERT: A 303 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9020 (tp) REVERT: C 11 SER cc_start: 0.8801 (m) cc_final: 0.8432 (t) REVERT: C 15 GLU cc_start: 0.7793 (pt0) cc_final: 0.7552 (pt0) REVERT: D 64 MET cc_start: 0.7992 (mmm) cc_final: 0.7738 (mmm) REVERT: E 22 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6944 (t0) REVERT: E 172 ASN cc_start: 0.8360 (t0) cc_final: 0.8142 (t0) REVERT: E 465 ASP cc_start: 0.8504 (m-30) cc_final: 0.7978 (t0) REVERT: F 169 GLU cc_start: 0.6792 (tp30) cc_final: 0.5904 (tp30) REVERT: F 459 MET cc_start: 0.7975 (tpp) cc_final: 0.7738 (tpp) REVERT: G 10 LEU cc_start: 0.9169 (tp) cc_final: 0.8814 (tp) REVERT: G 52 TYR cc_start: 0.7091 (m-80) cc_final: 0.6770 (m-10) REVERT: G 60 LEU cc_start: 0.7430 (mp) cc_final: 0.7217 (mp) REVERT: G 140 PHE cc_start: 0.8113 (t80) cc_final: 0.7779 (t80) REVERT: G 145 LEU cc_start: 0.8327 (mt) cc_final: 0.8118 (mt) REVERT: G 166 TYR cc_start: 0.8114 (p90) cc_final: 0.7079 (p90) REVERT: H 60 MET cc_start: 0.7052 (mpp) cc_final: 0.6786 (mpp) REVERT: H 83 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7516 (tt) REVERT: H 109 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8833 (mmmt) REVERT: I 13 TYR cc_start: 0.8826 (t80) cc_final: 0.8230 (t80) REVERT: Z 139 GLU cc_start: 0.6287 (tm-30) cc_final: 0.6081 (tm-30) REVERT: Z 140 LEU cc_start: 0.7381 (tp) cc_final: 0.7061 (mm) REVERT: Z 157 TRP cc_start: 0.6461 (m100) cc_final: 0.6119 (m100) REVERT: Z 159 ARG cc_start: 0.7342 (tmm160) cc_final: 0.6792 (ptt180) REVERT: Z 160 TYR cc_start: 0.6947 (t80) cc_final: 0.6463 (t80) REVERT: Z 166 GLN cc_start: 0.8021 (mm110) cc_final: 0.7570 (tp-100) REVERT: Z 170 ARG cc_start: 0.7589 (tmm160) cc_final: 0.6652 (tmm-80) REVERT: 7 100 MET cc_start: 0.7542 (mmp) cc_final: 0.6880 (tpp) REVERT: 7 121 LEU cc_start: 0.7605 (tp) cc_final: 0.7360 (pp) REVERT: 7 163 TYR cc_start: 0.5991 (t80) cc_final: 0.5164 (t80) REVERT: 7 173 MET cc_start: 0.7784 (mmt) cc_final: 0.7576 (mmm) REVERT: 8 10 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5858 (tmm) REVERT: X 46 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7156 (mm) REVERT: X 47 THR cc_start: 0.7392 (m) cc_final: 0.6056 (m) REVERT: X 57 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: X 58 TRP cc_start: 0.8004 (t-100) cc_final: 0.7151 (t-100) REVERT: X 94 MET cc_start: 0.7519 (tpp) cc_final: 0.6493 (mmm) REVERT: X 104 MET cc_start: 0.4443 (ptt) cc_final: 0.4163 (ttp) REVERT: X 169 ARG cc_start: 0.7852 (tmm-80) cc_final: 0.7072 (ttt180) REVERT: X 220 MET cc_start: 0.7871 (mmm) cc_final: 0.7347 (mmp) REVERT: J 1 MET cc_start: 0.1630 (tmm) cc_final: 0.0974 (tmm) REVERT: J 25 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4958 (m-80) outliers start: 120 outliers final: 84 residues processed: 567 average time/residue: 0.2068 time to fit residues: 200.4231 Evaluate side-chains 547 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 450 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 PHE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 38 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain J residue 25 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 436 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 446 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 282 optimal weight: 0.0670 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.118809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084509 restraints weight = 116717.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086435 restraints weight = 64429.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086718 restraints weight = 43126.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087240 restraints weight = 34018.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087349 restraints weight = 30914.208| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 39481 Z= 0.202 Angle : 0.707 17.185 53507 Z= 0.349 Chirality : 0.044 0.246 6349 Planarity : 0.004 0.067 6839 Dihedral : 6.394 177.046 5471 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.79 % Allowed : 16.89 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 5060 helix: 0.96 (0.10), residues: 2716 sheet: -0.60 (0.21), residues: 596 loop : -0.78 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 250 TYR 0.018 0.002 TYR E 281 PHE 0.033 0.002 PHE O 64 TRP 0.036 0.002 TRP X 234 HIS 0.008 0.001 HIS X 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (39481) covalent geometry : angle 0.70731 / 0.35 (53507) hydrogen bonds : bond 0.03643 / 2.44 ( 2169) hydrogen bonds : angle 4.72632 / 3.33 ( 6321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 472 time to evaluate : 1.156 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: K 20 LEU cc_start: 0.7617 (tp) cc_final: 0.7361 (mt) REVERT: K 30 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6737 (m-10) REVERT: K 48 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: L 67 MET cc_start: 0.7818 (tmm) cc_final: 0.7085 (tmm) REVERT: M 30 PHE cc_start: 0.7833 (m-80) cc_final: 0.7254 (m-10) REVERT: M 44 LYS cc_start: 0.8183 (pttt) cc_final: 0.7969 (ptmt) REVERT: M 50 MET cc_start: 0.7810 (tpp) cc_final: 0.7441 (tpp) REVERT: N 66 LEU cc_start: 0.3874 (OUTLIER) cc_final: 0.3541 (tp) REVERT: N 67 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4270 (ttt) REVERT: N 70 PHE cc_start: 0.6576 (m-10) cc_final: 0.5387 (t80) REVERT: O 19 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4794 (tt) REVERT: O 66 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5208 (mt) REVERT: P 53 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6985 (mp) REVERT: S 70 PHE cc_start: 0.8189 (m-80) cc_final: 0.7847 (m-80) REVERT: Y 34 ASP cc_start: 0.8461 (t0) cc_final: 0.8145 (t0) REVERT: Y 171 LEU cc_start: 0.8811 (tt) cc_final: 0.8581 (tp) REVERT: Y 192 GLU cc_start: 0.8168 (tp30) cc_final: 0.7821 (tp30) REVERT: A 303 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9011 (tp) REVERT: B 281 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8281 (ptt-90) REVERT: B 375 ARG cc_start: 0.7115 (mmt180) cc_final: 0.6829 (mmt180) REVERT: C 9 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5048 (mp0) REVERT: C 11 SER cc_start: 0.8844 (m) cc_final: 0.8525 (t) REVERT: C 15 GLU cc_start: 0.7855 (pt0) cc_final: 0.7613 (pt0) REVERT: E 22 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7110 (t0) REVERT: E 402 LEU cc_start: 0.8977 (tp) cc_final: 0.8654 (pp) REVERT: E 465 ASP cc_start: 0.8506 (m-30) cc_final: 0.7982 (t0) REVERT: F 459 MET cc_start: 0.8072 (tpp) cc_final: 0.7833 (tpp) REVERT: G 10 LEU cc_start: 0.9196 (tp) cc_final: 0.8889 (tp) REVERT: G 60 LEU cc_start: 0.7432 (mp) cc_final: 0.7225 (mp) REVERT: G 140 PHE cc_start: 0.8417 (t80) cc_final: 0.8158 (t80) REVERT: G 145 LEU cc_start: 0.8370 (mt) cc_final: 0.8133 (mt) REVERT: G 166 TYR cc_start: 0.8216 (p90) cc_final: 0.7066 (p90) REVERT: H 60 MET cc_start: 0.7110 (mpp) cc_final: 0.6824 (mpp) REVERT: H 83 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7478 (tt) REVERT: I 13 TYR cc_start: 0.8767 (t80) cc_final: 0.8029 (t80) REVERT: Z 139 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5892 (tm-30) REVERT: Z 140 LEU cc_start: 0.7328 (tp) cc_final: 0.6975 (mm) REVERT: Z 157 TRP cc_start: 0.6461 (m100) cc_final: 0.6147 (m100) REVERT: Z 159 ARG cc_start: 0.7380 (tmm160) cc_final: 0.6846 (ptt180) REVERT: Z 160 TYR cc_start: 0.7021 (t80) cc_final: 0.6550 (t80) REVERT: Z 170 ARG cc_start: 0.7613 (tmm160) cc_final: 0.6832 (tmm-80) REVERT: 7 121 LEU cc_start: 0.7568 (tp) cc_final: 0.7305 (pp) REVERT: 7 163 TYR cc_start: 0.6689 (t80) cc_final: 0.6103 (t80) REVERT: 8 10 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5516 (tmm) REVERT: 8 39 TYR cc_start: 0.5080 (m-10) cc_final: 0.4835 (m-10) REVERT: X 46 LEU cc_start: 0.7597 (pp) cc_final: 0.7157 (mm) REVERT: X 47 THR cc_start: 0.7134 (m) cc_final: 0.5695 (m) REVERT: X 57 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7509 (mtm-85) REVERT: X 58 TRP cc_start: 0.7955 (t-100) cc_final: 0.7152 (t-100) REVERT: X 62 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7058 (mt0) REVERT: X 104 MET cc_start: 0.4400 (ptt) cc_final: 0.4122 (ttp) REVERT: X 169 ARG cc_start: 0.7907 (tmm-80) cc_final: 0.6987 (ttt180) REVERT: X 188 MET cc_start: 0.6156 (mpp) cc_final: 0.5944 (mpp) REVERT: X 220 MET cc_start: 0.7963 (mmm) cc_final: 0.7417 (mmp) REVERT: J 1 MET cc_start: 0.1525 (tmm) cc_final: 0.0910 (tmm) REVERT: J 25 TYR cc_start: 0.5112 (OUTLIER) cc_final: 0.4749 (m-80) outliers start: 114 outliers final: 85 residues processed: 551 average time/residue: 0.2090 time to fit residues: 196.5150 Evaluate side-chains 544 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 444 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 PHE Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain Y residue 180 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain 7 residue 25 THR Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain J residue 25 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 447 optimal weight: 5.9990 chunk 403 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 371 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 441 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 GLN X 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.118989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084172 restraints weight = 115992.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086078 restraints weight = 61210.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087309 restraints weight = 39665.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088082 restraints weight = 29805.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088524 restraints weight = 24919.045| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39481 Z= 0.169 Angle : 0.698 14.132 53507 Z= 0.343 Chirality : 0.044 0.237 6349 Planarity : 0.004 0.066 6839 Dihedral : 6.375 173.560 5471 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 2.66 % Allowed : 17.30 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 5060 helix: 0.97 (0.10), residues: 2730 sheet: -0.60 (0.21), residues: 595 loop : -0.77 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 250 TYR 0.028 0.002 TYR 7 58 PHE 0.058 0.002 PHE Y 13 TRP 0.039 0.002 TRP X 234 HIS 0.008 0.001 HIS G 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (39481) covalent geometry : angle 0.69797 / 0.34 (53507) hydrogen bonds : bond 0.03589 / 2.40 ( 2169) hydrogen bonds : angle 4.70031 / 3.31 ( 6321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 457 time to evaluate : 1.563 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: K 20 LEU cc_start: 0.7503 (tp) cc_final: 0.7237 (mt) REVERT: K 30 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: K 48 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: L 67 MET cc_start: 0.7909 (tmm) cc_final: 0.7031 (tmm) REVERT: M 30 PHE cc_start: 0.7751 (m-80) cc_final: 0.7182 (m-10) REVERT: M 39 ARG cc_start: 0.7892 (ttm110) cc_final: 0.7571 (ttm170) REVERT: M 44 LYS cc_start: 0.8180 (pttt) cc_final: 0.7965 (ptmt) REVERT: M 50 MET cc_start: 0.7762 (tpp) cc_final: 0.7381 (tpp) REVERT: N 66 LEU cc_start: 0.3926 (OUTLIER) cc_final: 0.3652 (tp) REVERT: N 67 MET cc_start: 0.4826 (pp-130) cc_final: 0.4224 (mtt) REVERT: N 70 PHE cc_start: 0.6547 (m-10) cc_final: 0.5356 (t80) REVERT: O 19 LEU cc_start: 0.5250 (OUTLIER) cc_final: 0.4836 (tt) REVERT: O 66 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.5157 (mt) REVERT: P 53 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6963 (mp) REVERT: Q 50 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6393 (ppp) REVERT: S 45 ASP cc_start: 0.8437 (m-30) cc_final: 0.8224 (t0) REVERT: S 67 MET cc_start: 0.8077 (tpt) cc_final: 0.7525 (tpp) REVERT: S 70 PHE cc_start: 0.8189 (m-80) cc_final: 0.7770 (m-80) REVERT: Y 34 ASP cc_start: 0.8165 (t0) cc_final: 0.7856 (t0) REVERT: Y 60 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7347 (Cg_exo) REVERT: Y 192 GLU cc_start: 0.8105 (tp30) cc_final: 0.7720 (tp30) REVERT: A 218 LEU cc_start: 0.9384 (tt) cc_final: 0.9176 (tt) REVERT: A 303 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9086 (tp) REVERT: B 281 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8146 (ptt-90) REVERT: C 9 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5131 (mp0) REVERT: C 11 SER cc_start: 0.8819 (m) cc_final: 0.8538 (t) REVERT: C 15 GLU cc_start: 0.7843 (pt0) cc_final: 0.7623 (pt0) REVERT: D 64 MET cc_start: 0.8116 (mmm) cc_final: 0.7800 (tpp) REVERT: D 189 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6723 (mm-30) REVERT: E 22 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7052 (t0) REVERT: E 465 ASP cc_start: 0.8347 (m-30) cc_final: 0.7914 (t0) REVERT: F 414 LEU cc_start: 0.9002 (mt) cc_final: 0.8725 (mt) REVERT: F 459 MET cc_start: 0.8031 (tpp) cc_final: 0.7795 (tpp) REVERT: G 10 LEU cc_start: 0.9181 (tp) cc_final: 0.8866 (tp) REVERT: G 60 LEU cc_start: 0.7351 (mp) cc_final: 0.7137 (mp) REVERT: G 140 PHE cc_start: 0.8418 (t80) cc_final: 0.8110 (t80) REVERT: G 145 LEU cc_start: 0.8412 (mt) cc_final: 0.8208 (mt) REVERT: G 166 TYR cc_start: 0.8175 (p90) cc_final: 0.7234 (p90) REVERT: G 252 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8619 (t) REVERT: H 60 MET cc_start: 0.6824 (mpp) cc_final: 0.6596 (mpp) REVERT: H 83 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7651 (tt) REVERT: H 109 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8636 (mmmt) REVERT: I 13 TYR cc_start: 0.8712 (t80) cc_final: 0.8124 (t80) REVERT: Z 139 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5956 (tm-30) REVERT: Z 140 LEU cc_start: 0.7432 (tp) cc_final: 0.7067 (mm) REVERT: Z 159 ARG cc_start: 0.7093 (tmm160) cc_final: 0.6570 (ptt180) REVERT: Z 160 TYR cc_start: 0.7003 (t80) cc_final: 0.6594 (t80) REVERT: Z 170 ARG cc_start: 0.7549 (tmm160) cc_final: 0.6787 (tmm-80) REVERT: Z 179 ARG cc_start: 0.4245 (OUTLIER) cc_final: 0.3786 (mmp80) REVERT: 7 121 LEU cc_start: 0.7569 (tp) cc_final: 0.7311 (pp) REVERT: 7 163 TYR cc_start: 0.6500 (t80) cc_final: 0.5960 (t80) REVERT: 8 10 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.5771 (tmm) REVERT: 8 20 MET cc_start: 0.7204 (ppp) cc_final: 0.5202 (mtt) REVERT: X 46 LEU cc_start: 0.7589 (pp) cc_final: 0.7117 (mm) REVERT: X 47 THR cc_start: 0.7297 (m) cc_final: 0.5775 (m) REVERT: X 57 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: X 58 TRP cc_start: 0.7978 (t-100) cc_final: 0.7113 (t-100) REVERT: X 62 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: X 104 MET cc_start: 0.4425 (ptt) cc_final: 0.4114 (ttp) REVERT: X 169 ARG cc_start: 0.7873 (tmm-80) cc_final: 0.6944 (ttt180) REVERT: X 220 MET cc_start: 0.7984 (mmm) cc_final: 0.7479 (mmp) REVERT: J 1 MET cc_start: 0.1466 (tmm) cc_final: 0.0844 (tmm) REVERT: J 25 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.4647 (m-80) outliers start: 109 outliers final: 81 residues processed: 537 average time/residue: 0.2153 time to fit residues: 196.9489 Evaluate side-chains 539 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 441 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 PHE Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 55 PHE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 55 PHE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 50 MET Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 65 CYS Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain Y residue 62 LEU Chi-restraints excluded: chain Y residue 98 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 179 ARG Chi-restraints excluded: chain 7 residue 25 THR Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain 7 residue 83 ILE Chi-restraints excluded: chain 7 residue 165 ASP Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain 8 residue 10 MET Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 126 TRP Chi-restraints excluded: chain J residue 25 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 452 optimal weight: 5.9990 chunk 50 optimal weight: 50.0000 chunk 357 optimal weight: 0.9990 chunk 297 optimal weight: 9.9990 chunk 390 optimal weight: 0.0040 chunk 38 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 376 optimal weight: 0.0870 chunk 74 optimal weight: 7.9990 chunk 407 optimal weight: 10.0000 overall best weight: 1.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 35 ASN M 35 ASN N 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN Z 166 GLN 8 11 ASN X 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084951 restraints weight = 116276.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086810 restraints weight = 61164.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.088030 restraints weight = 39650.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088821 restraints weight = 29694.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089268 restraints weight = 24718.087| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39481 Z= 0.149 Angle : 0.698 16.013 53507 Z= 0.342 Chirality : 0.044 0.246 6349 Planarity : 0.004 0.067 6839 Dihedral : 6.348 177.484 5471 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 2.59 % Allowed : 17.38 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 5060 helix: 1.04 (0.10), residues: 2724 sheet: -0.56 (0.22), residues: 582 loop : -0.72 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 250 TYR 0.020 0.001 TYR E 368 PHE 0.034 0.002 PHE S 64 TRP 0.039 0.002 TRP X 234 HIS 0.008 0.001 HIS Z 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (39481) covalent geometry : angle 0.69774 / 0.34 (53507) hydrogen bonds : bond 0.03536 / 2.36 ( 2169) hydrogen bonds : angle 4.67155 / 3.29 ( 6321) =============================================================================== Job complete usr+sys time: 8064.70 seconds wall clock time: 139 minutes 48.50 seconds (8388.50 seconds total)