Starting phenix.real_space_refine on Mon Aug 25 11:01:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo0_36451/08_2025/8jo0_36451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo0_36451/08_2025/8jo0_36451.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/8jo0_36451/08_2025/8jo0_36451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo0_36451/08_2025/8jo0_36451.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo0_36451/08_2025/8jo0_36451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo0_36451/08_2025/8jo0_36451.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 199 5.16 5 C 17375 2.51 5 N 4579 2.21 5 O 5181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27362 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "C" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 374} Chain breaks: 2 Chain: "D" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "F" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "G" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.97, per 1000 atoms: 0.25 Number of scatterers: 27362 At special positions: 0 Unit cell: (161.04, 165, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 199 16.00 P 21 15.00 Mg 7 11.99 O 5181 8.00 N 4579 7.00 C 17375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6530 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 14 sheets defined 59.9% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.757A pdb=" N ALA H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 49 through 65 removed outlier: 3.557A pdb=" N ARG H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 65 " --> pdb=" O TYR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.524A pdb=" N PHE H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE H 86 " --> pdb=" O HIS H 82 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.978A pdb=" N GLN H 109 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 33 removed outlier: 3.756A pdb=" N ALA I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR I 28 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 46 Processing helix chain 'I' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 65 " --> pdb=" O TYR I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.524A pdb=" N PHE I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA I 94 " --> pdb=" O TYR I 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE I 95 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN I 96 " --> pdb=" O ASP I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 106 through 110 removed outlier: 3.979A pdb=" N GLN I 109 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU J 10 " --> pdb=" O GLU J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 33 removed outlier: 3.756A pdb=" N ALA J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 46 Processing helix chain 'J' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG J 53 " --> pdb=" O THR J 49 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA J 65 " --> pdb=" O TYR J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 removed outlier: 3.524A pdb=" N PHE J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA J 94 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE J 95 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN J 96 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 106 through 110 removed outlier: 3.978A pdb=" N GLN J 109 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 13 removed outlier: 3.631A pdb=" N LEU K 10 " --> pdb=" O GLU K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 20 removed outlier: 3.561A pdb=" N LEU K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 33 removed outlier: 3.774A pdb=" N ALA K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 46 Processing helix chain 'K' and resid 49 through 65 removed outlier: 3.554A pdb=" N ARG K 53 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG K 63 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA K 94 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 46 Processing helix chain 'L' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN L 64 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 65 " --> pdb=" O TYR L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 Processing helix chain 'L' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA L 94 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU M 10 " --> pdb=" O GLU M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 removed outlier: 3.559A pdb=" N LEU M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA M 26 " --> pdb=" O GLU M 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 46 Processing helix chain 'M' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG M 53 " --> pdb=" O THR M 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 63 " --> pdb=" O ARG M 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN M 64 " --> pdb=" O ILE M 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 Processing helix chain 'M' and resid 80 through 96 removed outlier: 3.617A pdb=" N ALA M 84 " --> pdb=" O GLN M 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE M 86 " --> pdb=" O HIS M 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA M 94 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.809A pdb=" N LYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.520A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.509A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.977A pdb=" N ILE A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.538A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.698A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.567A pdb=" N LEU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 4.419A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.653A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 457 through 466 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.812A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.808A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.516A pdb=" N SER B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.270A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.537A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.549A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.552A pdb=" N GLY B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.420A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.657A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 427 through 439 removed outlier: 4.041A pdb=" N ALA B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.954A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 487 removed outlier: 4.005A pdb=" N GLU B 481 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.955A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.809A pdb=" N LYS C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 173 Processing helix chain 'C' and resid 198 through 212 removed outlier: 4.270A pdb=" N PHE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.190A pdb=" N ILE C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 294 through 306 removed outlier: 3.538A pdb=" N TYR C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 326 removed outlier: 3.935A pdb=" N LYS C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 344 through 364 removed outlier: 3.570A pdb=" N LEU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 363 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 4.420A pdb=" N ARG C 380 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.663A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 428 through 439 removed outlier: 3.524A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 466 removed outlier: 4.147A pdb=" N LEU C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.812A pdb=" N ALA C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 535 removed outlier: 3.904A pdb=" N LEU C 535 " --> pdb=" O PHE C 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.810A pdb=" N LYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA D 238 " --> pdb=" O MET D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 4.326A pdb=" N ILE D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 306 removed outlier: 3.537A pdb=" N TYR D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 326 removed outlier: 3.789A pdb=" N LYS D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 344 through 355 removed outlier: 4.086A pdb=" N GLN D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 364 removed outlier: 3.572A pdb=" N GLY D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 363 " --> pdb=" O GLY D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 removed outlier: 4.420A pdb=" N ARG D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 removed outlier: 3.665A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 424 through 427 removed outlier: 3.735A pdb=" N ASP D 427 " --> pdb=" O GLU D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 424 through 427' Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 457 through 466 removed outlier: 4.170A pdb=" N LEU D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 486 removed outlier: 3.814A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 481 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 482 " --> pdb=" O SER D 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.809A pdb=" N LYS E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 176 removed outlier: 3.528A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET E 210 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA E 238 " --> pdb=" O MET E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 254 through 264 removed outlier: 3.984A pdb=" N ILE E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 294 through 306 removed outlier: 3.536A pdb=" N TYR E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 300 " --> pdb=" O ASP E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.960A pdb=" N LYS E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 344 through 364 removed outlier: 4.146A pdb=" N GLN E 350 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 362 " --> pdb=" O ARG E 358 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 363 " --> pdb=" O GLY E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 384 removed outlier: 3.765A pdb=" N ALA E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.666A pdb=" N SER E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 424 through 427 Processing helix chain 'E' and resid 428 through 439 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'E' and resid 469 through 485 removed outlier: 3.506A pdb=" N ILE E 473 " --> pdb=" O ASP E 469 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.599A pdb=" N ARG F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 removed outlier: 3.809A pdb=" N LYS F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 143 " --> pdb=" O ARG F 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 212 removed outlier: 4.270A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET F 210 " --> pdb=" O ASP F 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.508A pdb=" N ALA F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 255 through 265 Processing helix chain 'F' and resid 274 through 281 removed outlier: 4.203A pdb=" N ILE F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER F 278 " --> pdb=" O VAL F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.536A pdb=" N TYR F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 300 " --> pdb=" O ASP F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.811A pdb=" N ASN F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 321 " --> pdb=" O ASP F 317 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 340 Processing helix chain 'F' and resid 344 through 364 removed outlier: 8.820A pdb=" N LEU F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 384 removed outlier: 4.419A pdb=" N ARG F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 395 removed outlier: 3.665A pdb=" N SER F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 removed outlier: 3.586A pdb=" N CYS F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 439 removed outlier: 3.703A pdb=" N ALA F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 468 Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.961A pdb=" N ALA F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.810A pdb=" N LYS G 142 " --> pdb=" O ASP G 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS G 143 " --> pdb=" O ARG G 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 173 removed outlier: 3.521A pdb=" N ILE G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET G 210 " --> pdb=" O ASP G 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 211 " --> pdb=" O ILE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 226 Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA G 238 " --> pdb=" O MET G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 294 through 306 removed outlier: 3.537A pdb=" N TYR G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.696A pdb=" N LYS G 321 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER G 326 " --> pdb=" O THR G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 338 removed outlier: 3.641A pdb=" N PHE G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'G' and resid 359 through 364 removed outlier: 3.737A pdb=" N VAL G 363 " --> pdb=" O GLY G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 384 removed outlier: 3.518A pdb=" N ALA G 377 " --> pdb=" O SER G 373 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG G 380 " --> pdb=" O MET G 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS G 381 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 407 through 412 Processing helix chain 'G' and resid 427 through 440 removed outlier: 4.213A pdb=" N ALA G 431 " --> pdb=" O ASP G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 443 No H-bonds generated for 'chain 'G' and resid 441 through 443' Processing helix chain 'G' and resid 457 through 468 removed outlier: 4.262A pdb=" N LEU G 464 " --> pdb=" O ILE G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 486 Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 541 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.676A pdb=" N THR A 272 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.557A pdb=" N SER B 186 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 248 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 188 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP B 250 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 190 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 252 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG B 267 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 191 removed outlier: 6.554A pdb=" N SER C 186 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL C 248 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 188 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP C 250 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 190 " --> pdb=" O ASP C 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 252 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG C 267 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 272 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 191 removed outlier: 6.528A pdb=" N SER D 186 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL D 248 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 188 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP D 250 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 190 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL D 252 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 272 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE D 154 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 288 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 156 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 290 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS D 158 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AA9, first strand: chain 'E' and resid 187 through 191 removed outlier: 6.535A pdb=" N VAL E 188 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP E 250 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 190 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 252 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 272 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'F' and resid 186 through 191 removed outlier: 6.508A pdb=" N SER F 186 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL F 248 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL F 188 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP F 250 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU F 190 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 252 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 405 through 406 Processing sheet with id=AB4, first strand: chain 'G' and resid 187 through 191 removed outlier: 6.535A pdb=" N VAL G 188 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP G 250 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU G 190 " --> pdb=" O ASP G 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL G 252 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE G 247 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR G 271 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE G 249 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 155 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR G 272 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE G 154 " --> pdb=" O GLU G 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 405 through 406 1085 hydrogen bonds defined for protein. 3153 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: 5.12 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7938 1.33 - 1.46: 5781 1.46 - 1.59: 13798 1.59 - 1.72: 21 1.72 - 1.85: 316 Bond restraints: 27854 Sorted by residual: bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.31e+01 bond pdb=" C4 ATP G 602 " pdb=" C5 ATP G 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.24e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.13e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.10e+01 bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.04e+01 ... (remaining 27849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 37317 5.15 - 10.29: 337 10.29 - 15.44: 15 15.44 - 20.58: 0 20.58 - 25.73: 7 Bond angle restraints: 37676 Sorted by residual: angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 114.18 25.69 1.00e+00 1.00e+00 6.60e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 114.20 25.67 1.00e+00 1.00e+00 6.59e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 114.21 25.66 1.00e+00 1.00e+00 6.58e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.23 25.64 1.00e+00 1.00e+00 6.57e+02 ... (remaining 37671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 15155 25.73 - 51.46: 1581 51.46 - 77.20: 457 77.20 - 102.93: 39 102.93 - 128.66: 6 Dihedral angle restraints: 17238 sinusoidal: 7273 harmonic: 9965 Sorted by residual: dihedral pdb=" CA MET A 449 " pdb=" C MET A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta harmonic sigma weight residual -180.00 -51.34 -128.66 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" CA MET G 449 " pdb=" C MET G 449 " pdb=" N PRO G 450 " pdb=" CA PRO G 450 " ideal model delta harmonic sigma weight residual -180.00 -51.39 -128.61 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" CA MET B 449 " pdb=" C MET B 449 " pdb=" N PRO B 450 " pdb=" CA PRO B 450 " ideal model delta harmonic sigma weight residual -180.00 -51.40 -128.60 0 5.00e+00 4.00e-02 6.61e+02 ... (remaining 17235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2916 0.070 - 0.139: 1088 0.139 - 0.209: 263 0.209 - 0.279: 58 0.279 - 0.348: 12 Chirality restraints: 4337 Sorted by residual: chirality pdb=" CA PHE E 204 " pdb=" N PHE E 204 " pdb=" C PHE E 204 " pdb=" CB PHE E 204 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PHE C 532 " pdb=" N PHE C 532 " pdb=" C PHE C 532 " pdb=" CB PHE C 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 4334 not shown) Planarity restraints: 4780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 443 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C LEU B 443 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU B 443 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 444 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 148 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C CYS C 148 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS C 148 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP C 149 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 336 " 0.016 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE E 336 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE E 336 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE E 337 " 0.019 2.00e-02 2.50e+03 ... (remaining 4777 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 148 2.43 - 3.05: 20077 3.05 - 3.67: 41817 3.67 - 4.28: 64208 4.28 - 4.90: 99213 Nonbonded interactions: 225463 Sorted by model distance: nonbonded pdb=" OG1 THR A 367 " pdb=" CD PRO A 368 " model vdw 1.813 3.440 nonbonded pdb=" CD PRO A 530 " pdb=" NZ LYS A 531 " model vdw 1.994 3.520 nonbonded pdb=" CD PRO B 530 " pdb=" NZ LYS B 531 " model vdw 1.995 3.520 nonbonded pdb=" CD PRO E 530 " pdb=" NZ LYS E 531 " model vdw 1.995 3.520 nonbonded pdb=" CD PRO C 530 " pdb=" NZ LYS C 531 " model vdw 1.995 3.520 ... (remaining 225458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 105) selection = (chain 'I' and resid 1 through 105) selection = (chain 'J' and resid 1 through 105) selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.550 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 27854 Z= 0.644 Angle : 1.485 25.727 37676 Z= 1.071 Chirality : 0.076 0.348 4337 Planarity : 0.006 0.059 4780 Dihedral : 21.290 128.660 10708 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 62.06 Ramachandran Plot: Outliers : 1.50 % Allowed : 13.79 % Favored : 84.71 % Rotamer: Outliers : 27.27 % Allowed : 15.78 % Favored : 56.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: -4.82 (0.12), residues: 3328 helix: -3.40 (0.09), residues: 1803 sheet: -1.88 (0.31), residues: 259 loop : -2.89 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 273 TYR 0.022 0.003 TYR C 371 PHE 0.020 0.002 PHE F 345 TRP 0.023 0.004 TRP F 189 HIS 0.004 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00916 (27854) covalent geometry : angle 1.48473 (37676) hydrogen bonds : bond 0.25317 ( 1085) hydrogen bonds : angle 10.38412 ( 3153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 840 poor density : 329 time to evaluate : 1.172 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: 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: H 64 GLN cc_start: 0.2185 (OUTLIER) cc_final: 0.1945 (mm110) REVERT: I 56 ASN cc_start: 0.3494 (m-40) cc_final: 0.3228 (m-40) REVERT: I 106 ILE cc_start: 0.4356 (mm) cc_final: 0.3714 (mm) REVERT: J 77 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: K 35 ILE cc_start: -0.4836 (OUTLIER) cc_final: -0.5143 (mt) REVERT: L 35 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3588 (mp) REVERT: L 68 LEU cc_start: -0.0908 (OUTLIER) cc_final: -0.1853 (pp) REVERT: M 43 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6560 (mp) REVERT: M 68 LEU cc_start: -0.0093 (OUTLIER) cc_final: -0.1984 (tp) REVERT: M 77 TYR cc_start: 0.4656 (OUTLIER) cc_final: 0.3907 (p90) REVERT: A 126 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8911 (tptp) REVERT: A 290 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 296 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8681 (p0) REVERT: A 336 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.9027 (t80) REVERT: A 350 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: A 393 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 410 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.8429 (m-90) REVERT: A 426 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7799 (tp) REVERT: A 536 HIS cc_start: 0.7470 (m-70) cc_final: 0.6846 (m170) REVERT: B 203 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9363 (tp) REVERT: B 228 SER cc_start: 0.9446 (OUTLIER) cc_final: 0.9235 (p) REVERT: B 296 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8794 (p0) REVERT: B 369 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 445 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 540 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: C 290 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8276 (t) REVERT: C 316 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: C 350 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: C 369 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8247 (t80) REVERT: C 439 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9045 (mmtm) REVERT: D 117 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.9024 (mmp80) REVERT: D 135 TYR cc_start: 0.8766 (t80) cc_final: 0.8537 (t80) REVERT: D 351 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9152 (mt) REVERT: D 439 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9136 (mmtm) REVERT: E 244 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8612 (t0) REVERT: E 259 ARG cc_start: 0.9448 (OUTLIER) cc_final: 0.9247 (tpp-160) REVERT: E 290 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8402 (t) REVERT: F 117 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8738 (mmt90) REVERT: F 203 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9374 (tp) REVERT: F 221 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7039 (Cg_exo) REVERT: F 296 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (p0) REVERT: F 369 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8300 (t80) REVERT: G 264 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9085 (mt) REVERT: G 296 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8937 (p0) REVERT: G 316 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: G 397 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8523 (p) REVERT: G 410 TRP cc_start: 0.8764 (OUTLIER) cc_final: 0.8389 (m-90) REVERT: G 531 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.6717 (tptt) outliers start: 840 outliers final: 210 residues processed: 1066 average time/residue: 0.2030 time to fit residues: 334.0091 Evaluate side-chains 482 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 229 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 ARG Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 8 ARG Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 534 GLN Chi-restraints excluded: chain C residue 540 TYR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 533 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 244 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 285 CYS Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 410 TRP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 381 CYS Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0010 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.0470 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN I 34 ASN J 34 ASN J 56 ASN J 64 GLN K 34 ASN K 64 GLN L 34 ASN L 64 GLN M 34 ASN M 64 GLN A 123 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN A 244 ASN A 262 GLN A 283 GLN A 471 GLN B 123 ASN B 237 ASN B 244 ASN B 471 GLN B 482 GLN C 123 ASN C 237 ASN C 244 ASN C 471 GLN C 482 GLN D 123 ASN D 225 HIS ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 283 GLN D 471 GLN D 537 GLN E 123 ASN E 225 HIS E 237 ASN E 350 GLN E 471 GLN E 482 GLN F 123 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN F 244 ASN F 329 ASN F 352 ASN F 471 GLN F 475 ASN ** F 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN G 283 GLN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 458 HIS G 466 HIS G 471 GLN G 475 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.089051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.053001 restraints weight = 137670.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.050358 restraints weight = 123432.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.049495 restraints weight = 97645.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.049424 restraints weight = 81524.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.049480 restraints weight = 80446.181| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27854 Z= 0.175 Angle : 0.849 16.135 37676 Z= 0.424 Chirality : 0.046 0.203 4337 Planarity : 0.007 0.100 4780 Dihedral : 16.098 114.955 4408 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.66 % Favored : 94.89 % Rotamer: Outliers : 8.90 % Allowed : 22.89 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -3.07 (0.13), residues: 3328 helix: -1.91 (0.10), residues: 1875 sheet: -1.42 (0.31), residues: 224 loop : -2.11 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 525 TYR 0.030 0.002 TYR D 305 PHE 0.021 0.002 PHE I 93 TRP 0.022 0.002 TRP F 410 HIS 0.014 0.002 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00396 (27854) covalent geometry : angle 0.84870 (37676) hydrogen bonds : bond 0.05214 ( 1085) hydrogen bonds : angle 5.68684 ( 3153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 259 time to evaluate : 0.968 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: J 2 LEU cc_start: -0.4423 (mt) cc_final: -0.4695 (mt) REVERT: M 68 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4725 (tp) REVERT: A 203 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9411 (tt) REVERT: A 218 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7690 (pt) REVERT: A 228 SER cc_start: 0.9449 (m) cc_final: 0.9160 (p) REVERT: A 296 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8900 (p0) REVERT: A 410 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (m-90) REVERT: A 437 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9199 (mt) REVERT: A 536 HIS cc_start: 0.7718 (m-70) cc_final: 0.7373 (m170) REVERT: B 128 MET cc_start: 0.8674 (mmp) cc_final: 0.8044 (tpp) REVERT: B 218 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.7982 (pt) REVERT: B 398 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8284 (p) REVERT: C 135 TYR cc_start: 0.8235 (t80) cc_final: 0.8031 (t80) REVERT: C 218 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7633 (pt) REVERT: C 225 HIS cc_start: 0.9170 (m-70) cc_final: 0.8920 (m-70) REVERT: C 228 SER cc_start: 0.9613 (m) cc_final: 0.9410 (p) REVERT: C 317 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: C 335 MET cc_start: 0.9342 (mtt) cc_final: 0.8925 (mtt) REVERT: C 363 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8844 (p) REVERT: C 399 MET cc_start: 0.8619 (mmm) cc_final: 0.8087 (mmp) REVERT: C 439 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8888 (mmtm) REVERT: C 443 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8830 (pt) REVERT: C 444 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8426 (mm) REVERT: C 445 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7214 (t) REVERT: C 455 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9124 (ptmm) REVERT: C 531 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7684 (mmmt) REVERT: C 533 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8818 (tpp) REVERT: D 135 TYR cc_start: 0.8489 (t80) cc_final: 0.8252 (t80) REVERT: D 218 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.7875 (pt) REVERT: D 351 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9354 (mt) REVERT: D 355 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9518 (mm) REVERT: D 410 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.8714 (m-90) REVERT: D 462 MET cc_start: 0.9057 (mmp) cc_final: 0.8816 (mmp) REVERT: E 127 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8186 (pp30) REVERT: E 218 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.7874 (pt) REVERT: E 228 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9230 (p) REVERT: E 399 MET cc_start: 0.7624 (mpp) cc_final: 0.7070 (mmp) REVERT: F 210 MET cc_start: 0.9218 (tpp) cc_final: 0.8994 (tpp) REVERT: F 269 LEU cc_start: 0.9346 (tp) cc_final: 0.9102 (tp) REVERT: F 399 MET cc_start: 0.8397 (tpp) cc_final: 0.7988 (mmm) REVERT: G 128 MET cc_start: 0.8843 (mmm) cc_final: 0.8408 (mmm) REVERT: G 210 MET cc_start: 0.9303 (tpp) cc_final: 0.8888 (tpp) REVERT: G 218 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8382 (pt) REVERT: G 296 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8825 (p0) REVERT: G 315 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: G 531 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.7025 (tptt) outliers start: 274 outliers final: 117 residues processed: 517 average time/residue: 0.1722 time to fit residues: 144.8746 Evaluate side-chains 358 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 212 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 381 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 121 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 187 optimal weight: 0.0270 chunk 298 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 241 optimal weight: 0.0170 chunk 246 optimal weight: 9.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS E 113 GLN E 534 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.087537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.054686 restraints weight = 147440.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054444 restraints weight = 120059.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053006 restraints weight = 101481.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052128 restraints weight = 102513.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.052355 restraints weight = 82869.820| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27854 Z= 0.137 Angle : 0.727 19.784 37676 Z= 0.354 Chirality : 0.042 0.181 4337 Planarity : 0.006 0.060 4780 Dihedral : 12.959 117.131 4060 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.11 % Favored : 94.62 % Rotamer: Outliers : 5.88 % Allowed : 23.41 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.80 (0.14), residues: 3328 helix: -0.84 (0.12), residues: 1897 sheet: -1.37 (0.30), residues: 224 loop : -1.49 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 139 TYR 0.030 0.002 TYR D 305 PHE 0.014 0.001 PHE L 74 TRP 0.017 0.002 TRP E 410 HIS 0.011 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00306 (27854) covalent geometry : angle 0.72665 (37676) hydrogen bonds : bond 0.04026 ( 1085) hydrogen bonds : angle 4.82354 ( 3153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 226 time to evaluate : 1.143 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: H 2 LEU cc_start: -0.2774 (tt) cc_final: -0.2985 (mp) REVERT: I 46 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6450 (pttm) REVERT: J 2 LEU cc_start: -0.3431 (mt) cc_final: -0.3889 (mp) REVERT: J 44 ILE cc_start: 0.3145 (mt) cc_final: 0.2739 (mp) REVERT: J 62 ARG cc_start: 0.6668 (tmm160) cc_final: 0.6072 (mtp180) REVERT: L 1 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6535 (tpt) REVERT: L 47 MET cc_start: 0.2613 (mmt) cc_final: 0.1537 (tmm) REVERT: A 142 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8428 (pttm) REVERT: A 218 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7918 (pt) REVERT: A 228 SER cc_start: 0.9436 (m) cc_final: 0.9155 (p) REVERT: A 296 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8788 (p0) REVERT: A 459 ILE cc_start: 0.9482 (pt) cc_final: 0.9120 (mm) REVERT: B 128 MET cc_start: 0.8862 (mmp) cc_final: 0.8286 (tpp) REVERT: B 206 ASP cc_start: 0.8875 (m-30) cc_final: 0.8639 (m-30) REVERT: B 218 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8223 (pt) REVERT: B 277 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9070 (mt) REVERT: B 398 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8685 (p) REVERT: B 399 MET cc_start: 0.8188 (mmt) cc_final: 0.7761 (mmt) REVERT: C 128 MET cc_start: 0.8827 (mmt) cc_final: 0.8476 (mmt) REVERT: C 218 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8058 (pt) REVERT: C 335 MET cc_start: 0.9329 (mtt) cc_final: 0.9059 (mtt) REVERT: C 399 MET cc_start: 0.8806 (mmm) cc_final: 0.8552 (mmp) REVERT: C 439 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8841 (mmtm) REVERT: C 444 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8683 (mm) REVERT: C 455 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9127 (ptmm) REVERT: C 533 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8732 (tpp) REVERT: D 218 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8429 (pt) REVERT: D 355 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9424 (mm) REVERT: D 410 TRP cc_start: 0.9001 (OUTLIER) cc_final: 0.8666 (m-90) REVERT: D 449 MET cc_start: 0.8285 (pmm) cc_final: 0.8001 (pmm) REVERT: E 206 ASP cc_start: 0.8861 (m-30) cc_final: 0.8325 (m-30) REVERT: E 210 MET cc_start: 0.9023 (tpp) cc_final: 0.8714 (tpt) REVERT: E 218 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8277 (pt) REVERT: E 399 MET cc_start: 0.7830 (mpp) cc_final: 0.7443 (mmm) REVERT: F 198 LYS cc_start: 0.8755 (tppt) cc_final: 0.8541 (tppt) REVERT: F 210 MET cc_start: 0.9257 (tpp) cc_final: 0.9006 (tpp) REVERT: F 269 LEU cc_start: 0.9411 (tp) cc_final: 0.9140 (tp) REVERT: F 399 MET cc_start: 0.8595 (tpp) cc_final: 0.8198 (mmm) REVERT: G 128 MET cc_start: 0.8732 (mmm) cc_final: 0.8292 (mmm) REVERT: G 210 MET cc_start: 0.9241 (tpp) cc_final: 0.8644 (tpp) REVERT: G 218 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8164 (pt) REVERT: G 296 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8888 (p0) REVERT: G 449 MET cc_start: 0.8302 (pmm) cc_final: 0.8081 (pmm) REVERT: G 531 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.7398 (tptt) outliers start: 181 outliers final: 103 residues processed: 395 average time/residue: 0.1667 time to fit residues: 108.8445 Evaluate side-chains 314 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 191 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 381 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 212 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 99 optimal weight: 0.0060 chunk 123 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN I 40 HIS I 56 ASN J 40 HIS J 56 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 262 GLN D 237 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 HIS ** G 329 ASN ** 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 = 0.3704 r_free = 0.3704 target = 0.085595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.049040 restraints weight = 154625.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049004 restraints weight = 124046.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.048349 restraints weight = 93058.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.048349 restraints weight = 83711.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.048349 restraints weight = 83711.491| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27854 Z= 0.157 Angle : 0.693 13.687 37676 Z= 0.339 Chirality : 0.041 0.166 4337 Planarity : 0.005 0.061 4780 Dihedral : 12.072 115.465 4013 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 5.88 % Allowed : 23.54 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: -1.06 (0.15), residues: 3328 helix: -0.23 (0.12), residues: 1908 sheet: -1.09 (0.31), residues: 224 loop : -1.21 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 53 TYR 0.022 0.001 TYR D 305 PHE 0.014 0.001 PHE J 74 TRP 0.022 0.002 TRP A 410 HIS 0.016 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00348 (27854) covalent geometry : angle 0.69317 (37676) hydrogen bonds : bond 0.03654 ( 1085) hydrogen bonds : angle 4.52248 ( 3153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 194 time to evaluate : 1.265 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: H 58 LEU cc_start: 0.8602 (pp) cc_final: 0.8396 (mp) REVERT: I 46 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6538 (pttm) REVERT: L 1 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6442 (tpt) REVERT: L 47 MET cc_start: 0.2592 (mmt) cc_final: 0.1421 (tmm) REVERT: M 47 MET cc_start: 0.7146 (mmm) cc_final: 0.6259 (tmm) REVERT: A 206 ASP cc_start: 0.9031 (m-30) cc_final: 0.8782 (m-30) REVERT: A 212 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8650 (ttpt) REVERT: A 218 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8301 (pt) REVERT: A 296 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8888 (p0) REVERT: A 398 VAL cc_start: 0.9606 (OUTLIER) cc_final: 0.9193 (p) REVERT: A 399 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8427 (mmm) REVERT: B 128 MET cc_start: 0.9069 (mmp) cc_final: 0.8546 (tpp) REVERT: B 398 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.8829 (p) REVERT: B 399 MET cc_start: 0.8343 (mmt) cc_final: 0.7936 (mmp) REVERT: C 114 MET cc_start: 0.8567 (pmm) cc_final: 0.8200 (pmm) REVERT: C 218 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8407 (pt) REVERT: C 307 MET cc_start: 0.8718 (tpp) cc_final: 0.8299 (tpp) REVERT: C 372 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8742 (mmmt) REVERT: C 393 LEU cc_start: 0.9685 (tp) cc_final: 0.9348 (pp) REVERT: C 399 MET cc_start: 0.8800 (mmm) cc_final: 0.8568 (mmp) REVERT: C 439 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8783 (mmtm) REVERT: C 444 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8949 (mm) REVERT: C 455 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9089 (ptmm) REVERT: C 533 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8729 (tpp) REVERT: D 150 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9129 (mp) REVERT: D 218 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8362 (pt) REVERT: D 355 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9413 (mm) REVERT: D 410 TRP cc_start: 0.8926 (OUTLIER) cc_final: 0.8644 (m-90) REVERT: E 150 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8810 (tm) REVERT: E 206 ASP cc_start: 0.8998 (m-30) cc_final: 0.8528 (m-30) REVERT: E 399 MET cc_start: 0.8179 (mpp) cc_final: 0.7792 (mmm) REVERT: F 147 MET cc_start: 0.8336 (mtp) cc_final: 0.8108 (ptp) REVERT: F 198 LYS cc_start: 0.8684 (tppt) cc_final: 0.8447 (tppt) REVERT: F 206 ASP cc_start: 0.9022 (m-30) cc_final: 0.8817 (m-30) REVERT: F 210 MET cc_start: 0.9227 (tpp) cc_final: 0.9021 (tpp) REVERT: F 399 MET cc_start: 0.8714 (tpp) cc_final: 0.8224 (mmm) REVERT: F 533 MET cc_start: 0.8599 (ppp) cc_final: 0.7708 (ppp) REVERT: G 128 MET cc_start: 0.8861 (mmm) cc_final: 0.8572 (mmm) REVERT: G 210 MET cc_start: 0.9361 (tpp) cc_final: 0.8912 (tpp) REVERT: G 218 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (pt) REVERT: G 296 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8948 (p0) REVERT: G 531 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.7739 (tptt) outliers start: 181 outliers final: 108 residues processed: 362 average time/residue: 0.1759 time to fit residues: 104.1584 Evaluate side-chains 319 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 189 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 309 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 275 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN B 225 HIS C 262 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN G 536 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.083788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.046498 restraints weight = 149230.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044382 restraints weight = 126693.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.044519 restraints weight = 101603.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044972 restraints weight = 89821.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044789 restraints weight = 81276.061| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27854 Z= 0.212 Angle : 0.720 14.089 37676 Z= 0.350 Chirality : 0.041 0.175 4337 Planarity : 0.005 0.072 4780 Dihedral : 11.799 115.229 3983 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 5.81 % Allowed : 24.48 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: -0.68 (0.15), residues: 3328 helix: 0.16 (0.12), residues: 1887 sheet: -0.85 (0.31), residues: 224 loop : -1.20 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 63 TYR 0.015 0.002 TYR D 305 PHE 0.017 0.002 PHE F 532 TRP 0.020 0.002 TRP A 410 HIS 0.012 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00482 (27854) covalent geometry : angle 0.71974 (37676) hydrogen bonds : bond 0.03686 ( 1085) hydrogen bonds : angle 4.51260 ( 3153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 188 time to evaluate : 1.194 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: H 58 LEU cc_start: 0.8590 (pp) cc_final: 0.8341 (mp) REVERT: I 64 GLN cc_start: 0.3108 (OUTLIER) cc_final: 0.2160 (tm-30) REVERT: L 47 MET cc_start: 0.2949 (mmt) cc_final: 0.1742 (tmm) REVERT: M 47 MET cc_start: 0.7181 (mmm) cc_final: 0.6322 (tmm) REVERT: A 128 MET cc_start: 0.9194 (mmm) cc_final: 0.8711 (mtt) REVERT: A 206 ASP cc_start: 0.9103 (m-30) cc_final: 0.8810 (m-30) REVERT: A 212 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8638 (ttpt) REVERT: A 218 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (pt) REVERT: A 399 MET cc_start: 0.8927 (mmt) cc_final: 0.8393 (mmt) REVERT: B 128 MET cc_start: 0.9152 (mmp) cc_final: 0.8695 (tpp) REVERT: B 206 ASP cc_start: 0.9069 (m-30) cc_final: 0.8834 (m-30) REVERT: B 210 MET cc_start: 0.9025 (tpp) cc_final: 0.8649 (tpp) REVERT: B 334 MET cc_start: 0.9139 (tpp) cc_final: 0.8928 (tpp) REVERT: B 398 VAL cc_start: 0.9556 (OUTLIER) cc_final: 0.9167 (m) REVERT: C 218 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8478 (pt) REVERT: C 234 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8739 (mtm) REVERT: C 307 MET cc_start: 0.8790 (tpp) cc_final: 0.8249 (tpp) REVERT: C 399 MET cc_start: 0.8874 (mmm) cc_final: 0.8641 (mmp) REVERT: C 444 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8976 (mm) REVERT: C 449 MET cc_start: 0.9152 (mmm) cc_final: 0.8292 (pmm) REVERT: C 455 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9097 (ptmm) REVERT: C 533 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8949 (tpp) REVERT: D 150 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8942 (mp) REVERT: D 218 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (pt) REVERT: D 220 PHE cc_start: 0.9013 (p90) cc_final: 0.8810 (p90) REVERT: D 309 MET cc_start: 0.8974 (mmm) cc_final: 0.8663 (mmp) REVERT: D 410 TRP cc_start: 0.8989 (OUTLIER) cc_final: 0.8548 (m-90) REVERT: E 150 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8793 (tm) REVERT: E 206 ASP cc_start: 0.9019 (m-30) cc_final: 0.8598 (m-30) REVERT: E 210 MET cc_start: 0.9164 (tpp) cc_final: 0.8863 (tpt) REVERT: E 234 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8869 (mpp) REVERT: E 309 MET cc_start: 0.8906 (tpp) cc_final: 0.8175 (tpp) REVERT: E 399 MET cc_start: 0.8437 (tpp) cc_final: 0.8005 (mmm) REVERT: F 114 MET cc_start: 0.8744 (pmm) cc_final: 0.8521 (pmm) REVERT: F 198 LYS cc_start: 0.8742 (tppt) cc_final: 0.8518 (tppt) REVERT: F 393 LEU cc_start: 0.9742 (tp) cc_final: 0.9455 (pp) REVERT: F 410 TRP cc_start: 0.9137 (OUTLIER) cc_final: 0.8537 (m-90) REVERT: G 210 MET cc_start: 0.9324 (tpp) cc_final: 0.8931 (tpp) REVERT: G 218 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8451 (pt) REVERT: G 410 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.8411 (m-90) REVERT: G 531 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.7449 (tptt) outliers start: 179 outliers final: 108 residues processed: 353 average time/residue: 0.1837 time to fit residues: 105.2122 Evaluate side-chains 303 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 177 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 265 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 307 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 200 optimal weight: 0.0770 chunk 310 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 303 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS C 262 GLN E 262 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.084470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3118 r_free = 0.3118 target = 0.046036 restraints weight = 154067.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046175 restraints weight = 114678.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046289 restraints weight = 98832.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.047147 restraints weight = 90675.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.047147 restraints weight = 81814.250| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27854 Z= 0.128 Angle : 0.687 12.679 37676 Z= 0.326 Chirality : 0.040 0.182 4337 Planarity : 0.005 0.075 4780 Dihedral : 11.335 116.514 3965 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 5.00 % Allowed : 25.49 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: -0.36 (0.15), residues: 3328 helix: 0.32 (0.13), residues: 1918 sheet: -0.53 (0.29), residues: 259 loop : -0.95 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 390 TYR 0.017 0.001 TYR D 305 PHE 0.017 0.001 PHE I 36 TRP 0.014 0.001 TRP A 410 HIS 0.012 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00301 (27854) covalent geometry : angle 0.68672 (37676) hydrogen bonds : bond 0.03247 ( 1085) hydrogen bonds : angle 4.29493 ( 3153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 191 time to evaluate : 1.121 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: H 56 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7436 (p0) REVERT: H 58 LEU cc_start: 0.8647 (pp) cc_final: 0.8345 (mp) REVERT: H 68 LEU cc_start: 0.3163 (pt) cc_final: 0.2861 (mt) REVERT: L 47 MET cc_start: 0.2984 (mmt) cc_final: 0.2469 (tpp) REVERT: M 47 MET cc_start: 0.7151 (mmm) cc_final: 0.6269 (tmm) REVERT: A 206 ASP cc_start: 0.9102 (m-30) cc_final: 0.8790 (m-30) REVERT: A 212 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8667 (ttpt) REVERT: A 379 GLN cc_start: 0.9673 (OUTLIER) cc_final: 0.9039 (tm-30) REVERT: A 398 VAL cc_start: 0.9717 (OUTLIER) cc_final: 0.9110 (m) REVERT: A 399 MET cc_start: 0.8846 (mmt) cc_final: 0.8390 (mmt) REVERT: B 128 MET cc_start: 0.9123 (mmp) cc_final: 0.8895 (mmm) REVERT: B 210 MET cc_start: 0.8976 (tpp) cc_final: 0.8515 (tpp) REVERT: B 307 MET cc_start: 0.8952 (mmm) cc_final: 0.8508 (mmm) REVERT: C 114 MET cc_start: 0.8618 (pmm) cc_final: 0.8220 (pmm) REVERT: C 234 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8792 (mtm) REVERT: C 262 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8969 (tp-100) REVERT: C 307 MET cc_start: 0.8885 (tpp) cc_final: 0.8409 (tpp) REVERT: C 399 MET cc_start: 0.8937 (mmm) cc_final: 0.8729 (mmp) REVERT: C 444 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8860 (mm) REVERT: C 533 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8908 (tpp) REVERT: D 150 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8896 (mp) REVERT: D 410 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8546 (m-90) REVERT: E 150 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8682 (tm) REVERT: E 206 ASP cc_start: 0.9067 (m-30) cc_final: 0.8635 (m-30) REVERT: E 234 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8875 (mpp) REVERT: E 309 MET cc_start: 0.8857 (tpp) cc_final: 0.8134 (tpp) REVERT: E 399 MET cc_start: 0.8419 (tpp) cc_final: 0.8036 (mmm) REVERT: E 485 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7866 (pp) REVERT: F 114 MET cc_start: 0.8806 (pmm) cc_final: 0.8563 (pmm) REVERT: F 147 MET cc_start: 0.8608 (mtp) cc_final: 0.8231 (ptp) REVERT: F 198 LYS cc_start: 0.8702 (tppt) cc_final: 0.8439 (tppt) REVERT: F 206 ASP cc_start: 0.8958 (m-30) cc_final: 0.8732 (m-30) REVERT: F 348 MET cc_start: 0.9098 (mtt) cc_final: 0.8782 (ptp) REVERT: F 393 LEU cc_start: 0.9748 (tp) cc_final: 0.9482 (pp) REVERT: F 399 MET cc_start: 0.8903 (tpp) cc_final: 0.8440 (mmm) REVERT: F 410 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8684 (m-90) REVERT: G 128 MET cc_start: 0.9078 (mmm) cc_final: 0.8575 (mtt) REVERT: G 210 MET cc_start: 0.9310 (tpp) cc_final: 0.8965 (tpp) REVERT: G 410 TRP cc_start: 0.8842 (OUTLIER) cc_final: 0.8542 (m-90) REVERT: G 531 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.7480 (tptt) REVERT: G 535 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9366 (mm) outliers start: 154 outliers final: 102 residues processed: 330 average time/residue: 0.1580 time to fit residues: 85.7780 Evaluate side-chains 303 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 184 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 535 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 60 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 217 optimal weight: 0.0000 chunk 180 optimal weight: 8.9990 chunk 210 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 215 optimal weight: 0.2980 chunk 43 optimal weight: 50.0000 chunk 187 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN I 64 GLN J 19 HIS J 56 ASN A 225 HIS B 283 GLN C 262 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050734 restraints weight = 155121.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047406 restraints weight = 138822.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.047323 restraints weight = 99738.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.047135 restraints weight = 84646.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.047128 restraints weight = 84333.243| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27854 Z= 0.119 Angle : 0.692 12.737 37676 Z= 0.326 Chirality : 0.040 0.195 4337 Planarity : 0.005 0.067 4780 Dihedral : 10.741 116.834 3947 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 4.74 % Allowed : 25.55 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: -0.18 (0.15), residues: 3328 helix: 0.46 (0.13), residues: 1914 sheet: -0.37 (0.29), residues: 259 loop : -0.87 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 390 TYR 0.014 0.001 TYR D 305 PHE 0.033 0.001 PHE I 36 TRP 0.012 0.001 TRP A 410 HIS 0.012 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00281 (27854) covalent geometry : angle 0.69210 (37676) hydrogen bonds : bond 0.03064 ( 1085) hydrogen bonds : angle 4.21726 ( 3153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 190 time to evaluate : 1.174 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: H 33 LYS cc_start: 0.4641 (tptp) cc_final: 0.4353 (mtpt) REVERT: H 58 LEU cc_start: 0.8669 (pp) cc_final: 0.8401 (mp) REVERT: H 62 ARG cc_start: 0.6106 (ttm110) cc_final: 0.5701 (ttt90) REVERT: J 62 ARG cc_start: 0.6116 (ttp80) cc_final: 0.5503 (mtp180) REVERT: L 47 MET cc_start: 0.2852 (mmt) cc_final: 0.1736 (tmm) REVERT: A 128 MET cc_start: 0.9103 (mmm) cc_final: 0.8661 (mtm) REVERT: A 206 ASP cc_start: 0.9135 (m-30) cc_final: 0.8787 (m-30) REVERT: A 212 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8684 (ttpt) REVERT: A 379 GLN cc_start: 0.9686 (OUTLIER) cc_final: 0.9163 (tm-30) REVERT: A 398 VAL cc_start: 0.9748 (OUTLIER) cc_final: 0.9273 (m) REVERT: A 399 MET cc_start: 0.8865 (mmt) cc_final: 0.8293 (mmm) REVERT: B 128 MET cc_start: 0.9112 (mmp) cc_final: 0.8850 (mmm) REVERT: B 210 MET cc_start: 0.8944 (tpp) cc_final: 0.8498 (tpp) REVERT: B 307 MET cc_start: 0.8813 (mmm) cc_final: 0.8598 (mmm) REVERT: C 114 MET cc_start: 0.8681 (pmm) cc_final: 0.8313 (pmm) REVERT: C 234 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8769 (mtm) REVERT: C 262 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8963 (tp-100) REVERT: C 307 MET cc_start: 0.8868 (tpp) cc_final: 0.8341 (tpp) REVERT: C 399 MET cc_start: 0.8904 (mmm) cc_final: 0.8702 (mmp) REVERT: C 439 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8811 (mmtm) REVERT: C 444 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8795 (mm) REVERT: C 449 MET cc_start: 0.9154 (mmm) cc_final: 0.8353 (pmm) REVERT: C 533 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8851 (tpp) REVERT: D 150 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8847 (mp) REVERT: D 410 TRP cc_start: 0.8854 (OUTLIER) cc_final: 0.8597 (m-90) REVERT: E 150 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8744 (tm) REVERT: E 206 ASP cc_start: 0.8993 (m-30) cc_final: 0.8575 (m-30) REVERT: E 399 MET cc_start: 0.8459 (tpp) cc_final: 0.8195 (mmm) REVERT: E 485 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7951 (pp) REVERT: F 114 MET cc_start: 0.8812 (pmm) cc_final: 0.8548 (pmm) REVERT: F 147 MET cc_start: 0.8539 (mtp) cc_final: 0.8328 (ptp) REVERT: F 198 LYS cc_start: 0.8794 (tppt) cc_final: 0.8560 (tppt) REVERT: F 206 ASP cc_start: 0.8932 (m-30) cc_final: 0.8715 (m-30) REVERT: F 393 LEU cc_start: 0.9760 (tp) cc_final: 0.9498 (pp) REVERT: F 399 MET cc_start: 0.8885 (tpp) cc_final: 0.8481 (mmm) REVERT: F 410 TRP cc_start: 0.9117 (OUTLIER) cc_final: 0.8683 (m-90) REVERT: G 128 MET cc_start: 0.9274 (mmm) cc_final: 0.8584 (mtt) REVERT: G 210 MET cc_start: 0.9270 (tpp) cc_final: 0.8756 (tpp) REVERT: G 410 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.8500 (m-90) REVERT: G 531 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.7770 (tptt) outliers start: 146 outliers final: 102 residues processed: 319 average time/residue: 0.1738 time to fit residues: 90.9913 Evaluate side-chains 301 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 184 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 290 optimal weight: 0.9990 chunk 132 optimal weight: 0.0370 chunk 110 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 288 optimal weight: 0.0870 chunk 280 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN J 56 ASN A 225 HIS A 352 ASN C 262 GLN C 475 ASN D 482 GLN F 158 HIS F 352 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.049229 restraints weight = 148469.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.047935 restraints weight = 124986.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047301 restraints weight = 105184.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.046940 restraints weight = 102868.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.046883 restraints weight = 100031.822| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27854 Z= 0.114 Angle : 0.698 12.612 37676 Z= 0.326 Chirality : 0.040 0.197 4337 Planarity : 0.005 0.067 4780 Dihedral : 10.434 116.633 3943 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 3.80 % Allowed : 26.27 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: -0.09 (0.15), residues: 3328 helix: 0.51 (0.13), residues: 1896 sheet: -0.25 (0.29), residues: 259 loop : -0.81 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 390 TYR 0.014 0.001 TYR D 371 PHE 0.013 0.001 PHE H 110 TRP 0.036 0.001 TRP E 410 HIS 0.012 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00262 (27854) covalent geometry : angle 0.69844 (37676) hydrogen bonds : bond 0.02889 ( 1085) hydrogen bonds : angle 4.14195 ( 3153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 187 time to evaluate : 0.709 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: K 47 MET cc_start: 0.6394 (mmm) cc_final: 0.5541 (ptm) REVERT: L 47 MET cc_start: 0.2925 (mmt) cc_final: 0.1852 (tmm) REVERT: A 128 MET cc_start: 0.9079 (mmm) cc_final: 0.8656 (mtm) REVERT: A 206 ASP cc_start: 0.9162 (m-30) cc_final: 0.8831 (m-30) REVERT: A 212 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8546 (ttpt) REVERT: A 307 MET cc_start: 0.8111 (tpp) cc_final: 0.7873 (tpp) REVERT: A 398 VAL cc_start: 0.9727 (OUTLIER) cc_final: 0.9241 (m) REVERT: A 399 MET cc_start: 0.8843 (mmt) cc_final: 0.8123 (mmm) REVERT: A 462 MET cc_start: 0.9134 (mtp) cc_final: 0.8258 (ttm) REVERT: B 210 MET cc_start: 0.8987 (tpp) cc_final: 0.8516 (tpp) REVERT: B 449 MET cc_start: 0.8987 (pmm) cc_final: 0.8616 (ppp) REVERT: C 114 MET cc_start: 0.8616 (pmm) cc_final: 0.8272 (pmm) REVERT: C 262 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8912 (tp-100) REVERT: C 307 MET cc_start: 0.8881 (tpp) cc_final: 0.8311 (tpp) REVERT: C 393 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9262 (pp) REVERT: C 399 MET cc_start: 0.8905 (mmm) cc_final: 0.8686 (mmp) REVERT: C 439 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8747 (mmtm) REVERT: C 444 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8416 (mm) REVERT: C 449 MET cc_start: 0.9402 (mmm) cc_final: 0.8562 (pmm) REVERT: C 533 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8817 (tpp) REVERT: D 150 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8824 (mp) REVERT: D 410 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.8574 (m-90) REVERT: E 150 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8769 (tm) REVERT: E 206 ASP cc_start: 0.9024 (m-30) cc_final: 0.8604 (m-30) REVERT: E 399 MET cc_start: 0.8471 (tpp) cc_final: 0.8034 (mmm) REVERT: E 462 MET cc_start: 0.9234 (mtp) cc_final: 0.8920 (ptm) REVERT: F 114 MET cc_start: 0.8799 (pmm) cc_final: 0.8521 (pmm) REVERT: F 198 LYS cc_start: 0.8759 (tppt) cc_final: 0.8478 (tppt) REVERT: F 206 ASP cc_start: 0.8990 (m-30) cc_final: 0.8762 (m-30) REVERT: F 348 MET cc_start: 0.9129 (mtt) cc_final: 0.8884 (ptp) REVERT: F 393 LEU cc_start: 0.9624 (tp) cc_final: 0.9397 (pp) REVERT: F 399 MET cc_start: 0.8924 (tpp) cc_final: 0.8486 (mmm) REVERT: F 410 TRP cc_start: 0.9143 (OUTLIER) cc_final: 0.8609 (m-90) REVERT: G 128 MET cc_start: 0.9209 (mmm) cc_final: 0.8376 (mtt) REVERT: G 210 MET cc_start: 0.9277 (tpp) cc_final: 0.8749 (tpp) REVERT: G 410 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.8561 (m-90) REVERT: G 531 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8002 (tptt) REVERT: G 535 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9386 (mm) outliers start: 117 outliers final: 88 residues processed: 291 average time/residue: 0.1612 time to fit residues: 76.6640 Evaluate side-chains 287 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 185 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 535 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 148 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 201 optimal weight: 0.0970 chunk 289 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 328 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 303 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 56 ASN A 225 HIS C 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050692 restraints weight = 151122.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.049743 restraints weight = 141915.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047331 restraints weight = 101840.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046788 restraints weight = 101741.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047007 restraints weight = 93127.694| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27854 Z= 0.113 Angle : 0.705 13.519 37676 Z= 0.328 Chirality : 0.040 0.216 4337 Planarity : 0.005 0.068 4780 Dihedral : 10.249 115.210 3943 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 3.67 % Allowed : 26.17 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: 0.01 (0.15), residues: 3328 helix: 0.64 (0.13), residues: 1873 sheet: -0.16 (0.29), residues: 259 loop : -0.84 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 62 TYR 0.015 0.001 TYR B 540 PHE 0.015 0.001 PHE H 110 TRP 0.029 0.001 TRP E 410 HIS 0.014 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00264 (27854) covalent geometry : angle 0.70494 (37676) hydrogen bonds : bond 0.02828 ( 1085) hydrogen bonds : angle 4.12599 ( 3153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 192 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 8 ARG cc_start: 0.0986 (mmt180) cc_final: 0.0640 (mmt180) REVERT: K 47 MET cc_start: 0.6378 (mmm) cc_final: 0.5519 (ptm) REVERT: L 47 MET cc_start: 0.3060 (mmt) cc_final: 0.1970 (tmm) REVERT: M 47 MET cc_start: 0.7157 (mmm) cc_final: 0.6252 (ppp) REVERT: A 128 MET cc_start: 0.9163 (mmm) cc_final: 0.8631 (mtm) REVERT: A 206 ASP cc_start: 0.9106 (m-30) cc_final: 0.8767 (m-30) REVERT: A 212 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8657 (ttpt) REVERT: A 307 MET cc_start: 0.8108 (tpp) cc_final: 0.7860 (tpp) REVERT: A 398 VAL cc_start: 0.9741 (OUTLIER) cc_final: 0.9306 (m) REVERT: A 399 MET cc_start: 0.8811 (mmt) cc_final: 0.8145 (mmm) REVERT: A 462 MET cc_start: 0.9113 (mtp) cc_final: 0.8431 (ttm) REVERT: B 128 MET cc_start: 0.9085 (mmm) cc_final: 0.8610 (mmm) REVERT: B 210 MET cc_start: 0.8967 (tpp) cc_final: 0.8507 (tpp) REVERT: B 307 MET cc_start: 0.8416 (mmm) cc_final: 0.7427 (mmm) REVERT: C 114 MET cc_start: 0.8635 (pmm) cc_final: 0.8311 (pmm) REVERT: C 234 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8802 (mtm) REVERT: C 262 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8931 (tp-100) REVERT: C 307 MET cc_start: 0.8872 (tpp) cc_final: 0.8268 (tpp) REVERT: C 393 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9338 (pp) REVERT: C 444 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8565 (mm) REVERT: C 449 MET cc_start: 0.9300 (mmm) cc_final: 0.8458 (pmm) REVERT: C 533 MET cc_start: 0.9090 (mmp) cc_final: 0.8876 (tpp) REVERT: D 150 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8789 (mp) REVERT: D 309 MET cc_start: 0.8636 (mmm) cc_final: 0.8363 (tpp) REVERT: D 393 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9447 (pp) REVERT: D 410 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.8617 (m-90) REVERT: D 533 MET cc_start: 0.8216 (mmm) cc_final: 0.8013 (mmm) REVERT: E 150 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8787 (tm) REVERT: E 206 ASP cc_start: 0.9083 (m-30) cc_final: 0.8645 (m-30) REVERT: E 399 MET cc_start: 0.8448 (tpp) cc_final: 0.8081 (mmm) REVERT: E 462 MET cc_start: 0.9203 (mtp) cc_final: 0.8913 (ptm) REVERT: F 114 MET cc_start: 0.8750 (pmm) cc_final: 0.8472 (pmm) REVERT: F 198 LYS cc_start: 0.8864 (tppt) cc_final: 0.8544 (tppt) REVERT: F 206 ASP cc_start: 0.8986 (m-30) cc_final: 0.8743 (m-30) REVERT: F 348 MET cc_start: 0.9092 (mtt) cc_final: 0.8865 (ptp) REVERT: F 393 LEU cc_start: 0.9718 (tp) cc_final: 0.9333 (pp) REVERT: F 399 MET cc_start: 0.8825 (tpp) cc_final: 0.8467 (mmm) REVERT: F 410 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8609 (m-90) REVERT: G 128 MET cc_start: 0.9250 (mmm) cc_final: 0.8307 (mtt) REVERT: G 210 MET cc_start: 0.9249 (tpp) cc_final: 0.8743 (tpp) REVERT: G 410 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8608 (m-90) REVERT: G 531 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.7832 (tptt) REVERT: G 535 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9393 (mm) outliers start: 113 outliers final: 93 residues processed: 293 average time/residue: 0.1663 time to fit residues: 80.2602 Evaluate side-chains 293 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 186 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 535 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 251 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 289 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN B 183 ASN B 237 ASN B 350 GLN C 262 GLN E 237 ASN F 352 ASN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044091 restraints weight = 151153.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.043696 restraints weight = 126959.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043396 restraints weight = 109079.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043482 restraints weight = 108761.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043475 restraints weight = 109748.687| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27854 Z= 0.219 Angle : 0.751 12.395 37676 Z= 0.360 Chirality : 0.041 0.182 4337 Planarity : 0.005 0.064 4780 Dihedral : 10.405 113.387 3940 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 3.73 % Allowed : 26.33 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: 0.00 (0.15), residues: 3328 helix: 0.65 (0.13), residues: 1908 sheet: -0.03 (0.29), residues: 259 loop : -0.95 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 62 TYR 0.017 0.002 TYR A 305 PHE 0.050 0.002 PHE I 36 TRP 0.037 0.002 TRP E 410 HIS 0.032 0.002 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00491 (27854) covalent geometry : angle 0.75051 (37676) hydrogen bonds : bond 0.03341 ( 1085) hydrogen bonds : angle 4.40661 ( 3153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 188 time to evaluate : 1.076 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: H 60 ILE cc_start: 0.4660 (tp) cc_final: 0.4274 (tp) REVERT: K 47 MET cc_start: 0.6453 (mmm) cc_final: 0.5597 (ptm) REVERT: L 47 MET cc_start: 0.2911 (mmt) cc_final: 0.1848 (tmm) REVERT: A 128 MET cc_start: 0.9181 (mmm) cc_final: 0.8597 (mtt) REVERT: A 206 ASP cc_start: 0.9147 (m-30) cc_final: 0.8846 (m-30) REVERT: A 212 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8663 (ttpt) REVERT: A 307 MET cc_start: 0.8244 (tpp) cc_final: 0.7953 (tpp) REVERT: A 398 VAL cc_start: 0.9790 (OUTLIER) cc_final: 0.9583 (m) REVERT: B 128 MET cc_start: 0.9183 (mmm) cc_final: 0.8923 (mmm) REVERT: B 210 MET cc_start: 0.9081 (tpp) cc_final: 0.8738 (tpp) REVERT: B 307 MET cc_start: 0.8519 (mmm) cc_final: 0.8055 (mmm) REVERT: B 348 MET cc_start: 0.9271 (ppp) cc_final: 0.8928 (ppp) REVERT: B 410 TRP cc_start: 0.9120 (OUTLIER) cc_final: 0.8726 (m-90) REVERT: C 234 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8761 (mtm) REVERT: C 262 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9038 (tp-100) REVERT: C 307 MET cc_start: 0.8908 (tpp) cc_final: 0.8307 (tpp) REVERT: C 444 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9056 (mm) REVERT: C 533 MET cc_start: 0.9243 (mmp) cc_final: 0.9002 (tpp) REVERT: D 150 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8975 (mm) REVERT: D 316 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8389 (mm-30) REVERT: D 393 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9462 (pp) REVERT: D 410 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8510 (m-90) REVERT: E 150 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8753 (tm) REVERT: E 198 LYS cc_start: 0.8690 (tppt) cc_final: 0.8298 (tppt) REVERT: E 206 ASP cc_start: 0.9139 (m-30) cc_final: 0.8746 (m-30) REVERT: E 234 MET cc_start: 0.9304 (mtm) cc_final: 0.9054 (mtm) REVERT: E 399 MET cc_start: 0.8483 (tpp) cc_final: 0.7886 (mmm) REVERT: F 114 MET cc_start: 0.8769 (pmm) cc_final: 0.8493 (pmm) REVERT: F 198 LYS cc_start: 0.8880 (tppt) cc_final: 0.8627 (tppt) REVERT: F 206 ASP cc_start: 0.9055 (m-30) cc_final: 0.8852 (m-30) REVERT: F 348 MET cc_start: 0.9164 (mtt) cc_final: 0.8870 (ptp) REVERT: F 399 MET cc_start: 0.8983 (tpp) cc_final: 0.8666 (mmm) REVERT: F 410 TRP cc_start: 0.9170 (OUTLIER) cc_final: 0.8594 (m-90) REVERT: G 128 MET cc_start: 0.9241 (mmm) cc_final: 0.8703 (mtt) REVERT: G 234 MET cc_start: 0.9206 (mtm) cc_final: 0.8952 (mtm) REVERT: G 348 MET cc_start: 0.9418 (ptp) cc_final: 0.9044 (ptp) REVERT: G 379 GLN cc_start: 0.9589 (OUTLIER) cc_final: 0.9301 (tm-30) REVERT: G 410 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8475 (m-90) REVERT: G 531 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.7892 (tptt) REVERT: G 535 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9360 (mm) outliers start: 115 outliers final: 87 residues processed: 296 average time/residue: 0.1485 time to fit residues: 72.1475 Evaluate side-chains 287 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 184 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 535 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 50 optimal weight: 50.0000 chunk 164 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 293 optimal weight: 0.3980 chunk 121 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 GLN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.082958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051984 restraints weight = 161193.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050278 restraints weight = 124740.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050396 restraints weight = 90727.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050391 restraints weight = 77914.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050404 restraints weight = 77664.000| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27854 Z= 0.144 Angle : 0.722 12.532 37676 Z= 0.338 Chirality : 0.041 0.194 4337 Planarity : 0.005 0.065 4780 Dihedral : 10.377 108.388 3940 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 3.47 % Allowed : 27.01 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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 aren not related in a simple way. whole: 0.17 (0.15), residues: 3328 helix: 0.78 (0.13), residues: 1915 sheet: -0.03 (0.29), residues: 259 loop : -0.89 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 62 TYR 0.015 0.001 TYR A 305 PHE 0.044 0.001 PHE I 36 TRP 0.032 0.002 TRP E 410 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00334 (27854) covalent geometry : angle 0.72164 (37676) hydrogen bonds : bond 0.03037 ( 1085) hydrogen bonds : angle 4.26452 ( 3153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7607.24 seconds wall clock time: 131 minutes 6.59 seconds (7866.59 seconds total)