Starting phenix.real_space_refine on Mon Jun 23 18:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo0_36451/06_2025/8jo0_36451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo0_36451/06_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_36451/06_2025/8jo0_36451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo0_36451/06_2025/8jo0_36451.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo0_36451/06_2025/8jo0_36451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo0_36451/06_2025/8jo0_36451.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.31, per 1000 atoms: 0.60 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: 6.79 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.61 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: 8.90 Time building geometry restraints manager: 8.07 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: 0.04 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 59.110 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.004 TRP F 189 HIS 0.004 0.001 HIS A 536 PHE 0.020 0.002 PHE F 345 TYR 0.022 0.003 TYR C 371 ARG 0.004 0.000 ARG E 273 Details of bonding type rmsd hydrogen bonds : bond 0.25317 ( 1085) hydrogen bonds : angle 10.38412 ( 3153) covalent geometry : bond 0.00916 (27854) covalent geometry : angle 1.48473 (37676) *********************** 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 : 2.991 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: 0.4213 time to fit residues: 688.7482 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 : 3.777 ------------------------------------------------------------------------------- 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 283 optimal weight: 0.7980 chunk 254 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 305 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C 534 GLN D 123 ASN D 225 HIS ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN D 471 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 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: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.087756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058263 restraints weight = 138074.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051762 restraints weight = 127953.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050034 restraints weight = 118428.364| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 27854 Z= 0.196 Angle : 0.850 15.956 37676 Z= 0.428 Chirality : 0.046 0.211 4337 Planarity : 0.007 0.104 4780 Dihedral : 16.244 112.349 4408 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.11 % Favored : 94.44 % Rotamer: Outliers : 9.29 % Allowed : 22.99 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.13), residues: 3328 helix: -1.98 (0.10), residues: 1903 sheet: -1.39 (0.31), residues: 224 loop : -1.97 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 410 HIS 0.014 0.002 HIS E 536 PHE 0.020 0.002 PHE I 93 TYR 0.032 0.002 TYR A 305 ARG 0.013 0.001 ARG A 525 Details of bonding type rmsd hydrogen bonds : bond 0.05497 ( 1085) hydrogen bonds : angle 5.83203 ( 3153) covalent geometry : bond 0.00453 (27854) covalent geometry : angle 0.84987 (37676) *********************** 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: 286 poor density : 247 time to evaluate : 3.167 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: H 56 ASN cc_start: 0.7479 (m110) cc_final: 0.7238 (m110) REVERT: J 2 LEU cc_start: -0.2760 (mt) cc_final: -0.3056 (mt) REVERT: L 68 LEU cc_start: 0.4376 (OUTLIER) cc_final: 0.4104 (pp) REVERT: M 68 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4876 (tp) REVERT: A 203 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9432 (tt) REVERT: A 218 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7739 (pt) REVERT: A 296 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8854 (p0) REVERT: A 410 TRP cc_start: 0.8843 (OUTLIER) cc_final: 0.8475 (m-90) REVERT: A 437 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9219 (mt) REVERT: B 128 MET cc_start: 0.8745 (mmp) cc_final: 0.8220 (mmt) REVERT: B 218 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.7997 (pt) REVERT: B 398 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 410 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8674 (m-90) REVERT: C 218 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7732 (pt) REVERT: C 225 HIS cc_start: 0.9183 (m-70) cc_final: 0.8903 (m-70) REVERT: C 317 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: C 335 MET cc_start: 0.9342 (mtt) cc_final: 0.8972 (mtt) REVERT: C 350 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: C 363 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8794 (p) REVERT: C 399 MET cc_start: 0.8777 (mmm) cc_final: 0.8558 (mmp) REVERT: C 410 TRP cc_start: 0.9334 (OUTLIER) cc_final: 0.8776 (m-90) REVERT: C 439 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9001 (mmtm) REVERT: C 443 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8918 (pt) REVERT: C 444 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8554 (mm) REVERT: C 445 SER cc_start: 0.7970 (OUTLIER) cc_final: 0.7476 (t) REVERT: C 455 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9110 (ptmm) REVERT: C 531 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7666 (mmmt) REVERT: C 533 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8848 (tpp) REVERT: D 135 TYR cc_start: 0.8585 (t80) cc_final: 0.8321 (t80) REVERT: D 218 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7714 (pt) REVERT: D 351 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9281 (mt) REVERT: D 355 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9520 (mm) REVERT: D 410 TRP cc_start: 0.9139 (OUTLIER) cc_final: 0.8568 (m-90) REVERT: D 462 MET cc_start: 0.9093 (mmp) cc_final: 0.8863 (mmp) REVERT: E 127 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8242 (pp30) REVERT: E 218 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7568 (pt) REVERT: E 228 SER cc_start: 0.9557 (OUTLIER) cc_final: 0.9275 (p) REVERT: E 399 MET cc_start: 0.7659 (mpp) cc_final: 0.7143 (mmp) REVERT: F 210 MET cc_start: 0.9229 (tpp) cc_final: 0.8975 (tpp) REVERT: F 269 LEU cc_start: 0.9431 (tp) cc_final: 0.9161 (tp) REVERT: F 399 MET cc_start: 0.8517 (tpp) cc_final: 0.8105 (mmm) REVERT: G 115 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8228 (mm) REVERT: G 116 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8411 (p0) REVERT: G 128 MET cc_start: 0.8860 (mmm) cc_final: 0.8258 (mmm) REVERT: G 210 MET cc_start: 0.9290 (tpp) cc_final: 0.8926 (tpp) REVERT: G 218 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8400 (pt) REVERT: G 315 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: G 410 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8809 (m-90) outliers start: 286 outliers final: 120 residues processed: 517 average time/residue: 0.3545 time to fit residues: 297.3218 Evaluate side-chains 346 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 192 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 77 TYR 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 68 LEU 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 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 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 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 TRP 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 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 426 LEU 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 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 157 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 480 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 285 CYS 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 460 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 115 LEU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 167 VAL 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 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 410 TRP 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 18 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 335 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 318 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 40 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN C 262 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** F 158 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.049261 restraints weight = 149198.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.048982 restraints weight = 122224.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047482 restraints weight = 103591.114| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27854 Z= 0.182 Angle : 0.733 19.184 37676 Z= 0.366 Chirality : 0.042 0.229 4337 Planarity : 0.006 0.066 4780 Dihedral : 13.205 117.675 4069 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 6.30 % Allowed : 23.54 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3328 helix: -0.75 (0.11), residues: 1908 sheet: -1.28 (0.30), residues: 224 loop : -1.65 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 410 HIS 0.011 0.001 HIS E 536 PHE 0.016 0.002 PHE I 93 TYR 0.030 0.002 TYR D 305 ARG 0.014 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 1085) hydrogen bonds : angle 4.92332 ( 3153) covalent geometry : bond 0.00413 (27854) covalent geometry : angle 0.73341 (37676) *********************** 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 405 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 211 time to evaluate : 3.055 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: I 46 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6474 (pttm) REVERT: L 1 MET cc_start: 0.6951 (mmp) cc_final: 0.6371 (tpt) REVERT: L 47 MET cc_start: 0.2532 (mmt) cc_final: 0.1572 (tmm) REVERT: L 68 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.4289 (pp) REVERT: A 142 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8672 (ptpp) REVERT: A 218 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8072 (pt) REVERT: A 296 ASP cc_start: 0.9346 (OUTLIER) cc_final: 0.9052 (p0) REVERT: A 348 MET cc_start: 0.9207 (ppp) cc_final: 0.9005 (ppp) REVERT: A 410 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.8587 (m-90) REVERT: B 128 MET cc_start: 0.9051 (mmp) cc_final: 0.8481 (tpp) REVERT: B 210 MET cc_start: 0.8983 (tpp) cc_final: 0.8660 (tpp) REVERT: B 218 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8292 (pt) REVERT: B 410 TRP cc_start: 0.9111 (OUTLIER) cc_final: 0.8604 (m-90) REVERT: C 218 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8221 (pt) REVERT: C 262 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8659 (tp-100) REVERT: C 410 TRP cc_start: 0.9174 (OUTLIER) cc_final: 0.8808 (m-90) REVERT: C 439 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8888 (mmtm) REVERT: C 444 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8928 (mm) REVERT: C 533 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8931 (tpp) REVERT: D 198 LYS cc_start: 0.8806 (tppt) cc_final: 0.8576 (tppt) REVERT: D 218 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8308 (pt) REVERT: D 351 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9414 (mt) REVERT: D 355 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9458 (mm) REVERT: D 410 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.8583 (m-90) REVERT: D 449 MET cc_start: 0.8439 (pmm) cc_final: 0.8144 (pmm) REVERT: D 462 MET cc_start: 0.9015 (mmp) cc_final: 0.8811 (mmp) REVERT: E 210 MET cc_start: 0.9164 (tpp) cc_final: 0.8856 (tpt) REVERT: E 218 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8441 (pt) REVERT: E 262 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8821 (tp-100) REVERT: E 399 MET cc_start: 0.8077 (mpp) cc_final: 0.7614 (mmm) REVERT: F 198 LYS cc_start: 0.8997 (tppt) cc_final: 0.8738 (tppt) REVERT: F 210 MET cc_start: 0.9244 (tpp) cc_final: 0.8990 (tpp) REVERT: F 399 MET cc_start: 0.8718 (tpp) cc_final: 0.8082 (mmt) REVERT: F 533 MET cc_start: 0.8553 (ppp) cc_final: 0.7674 (ppp) REVERT: G 128 MET cc_start: 0.8852 (mmm) cc_final: 0.8489 (mmm) REVERT: G 210 MET cc_start: 0.9331 (tpp) cc_final: 0.8879 (tpp) REVERT: G 218 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8346 (pt) REVERT: G 315 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: G 410 TRP cc_start: 0.9026 (OUTLIER) cc_final: 0.8591 (m-90) outliers start: 194 outliers final: 113 residues processed: 393 average time/residue: 0.3521 time to fit residues: 224.3304 Evaluate side-chains 321 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 185 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 77 TYR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR 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 140 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 192 ASP 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 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 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 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 141 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 205 THR 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 314 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS 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 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 B residue 542 SER 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 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 374 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 410 TRP 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 459 ILE 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 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 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 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 459 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 205 THR 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 262 GLN Chi-restraints excluded: chain E residue 360 LEU 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 460 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE 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 219 ASN Chi-restraints excluded: chain F residue 256 GLU 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 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 140 VAL 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 248 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 290 VAL 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 393 LEU Chi-restraints excluded: chain G residue 397 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 135 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 309 optimal weight: 0.3980 chunk 255 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 246 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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 40 HIS J 56 ASN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN A 352 ASN C 262 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 237 ASN D 536 HIS E 534 GLN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051685 restraints weight = 155247.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049076 restraints weight = 152111.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048066 restraints weight = 111446.163| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 27854 Z= 0.226 Angle : 0.729 12.862 37676 Z= 0.362 Chirality : 0.042 0.172 4337 Planarity : 0.006 0.062 4780 Dihedral : 12.448 118.068 4031 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 6.75 % Allowed : 22.99 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3328 helix: -0.23 (0.12), residues: 1934 sheet: -0.85 (0.28), residues: 259 loop : -1.41 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 410 HIS 0.010 0.002 HIS A 225 PHE 0.019 0.002 PHE F 532 TYR 0.024 0.002 TYR D 305 ARG 0.024 0.001 ARG J 53 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 1085) hydrogen bonds : angle 4.78640 ( 3153) covalent geometry : bond 0.00507 (27854) covalent geometry : angle 0.72906 (37676) *********************** 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 401 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 193 time to evaluate : 3.019 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: L 1 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6447 (tpt) REVERT: L 47 MET cc_start: 0.2644 (mmt) cc_final: 0.1564 (tmm) REVERT: M 47 MET cc_start: 0.7155 (mmm) cc_final: 0.6298 (tmm) REVERT: A 128 MET cc_start: 0.9178 (mmm) cc_final: 0.8656 (mtm) REVERT: A 206 ASP cc_start: 0.9042 (m-30) cc_final: 0.8771 (m-30) REVERT: A 212 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8716 (ttpt) REVERT: A 218 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8417 (pt) REVERT: A 262 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.9074 (tt0) REVERT: A 410 TRP cc_start: 0.9094 (OUTLIER) cc_final: 0.8665 (m-90) REVERT: B 128 MET cc_start: 0.9178 (mmp) cc_final: 0.8894 (mmp) REVERT: B 210 MET cc_start: 0.9081 (tpp) cc_final: 0.8656 (tpp) REVERT: B 262 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8902 (pp30) REVERT: B 351 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9275 (mt) REVERT: B 398 VAL cc_start: 0.9509 (OUTLIER) cc_final: 0.9275 (m) REVERT: B 410 TRP cc_start: 0.9106 (OUTLIER) cc_final: 0.8565 (m-90) REVERT: B 543 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5855 (pp) REVERT: C 114 MET cc_start: 0.8578 (pmm) cc_final: 0.8175 (pmm) REVERT: C 218 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8728 (pt) REVERT: C 410 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8670 (m-90) REVERT: C 439 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8673 (mmtm) REVERT: C 444 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9112 (mm) REVERT: C 533 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.9018 (tpp) REVERT: D 150 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8912 (mp) REVERT: D 307 MET cc_start: 0.8544 (tmm) cc_final: 0.8265 (mmm) REVERT: D 351 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9452 (mt) REVERT: D 355 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9578 (mm) REVERT: D 410 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.8492 (m-90) REVERT: E 150 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8826 (tm) REVERT: E 198 LYS cc_start: 0.8885 (tppt) cc_final: 0.8518 (tppt) REVERT: E 399 MET cc_start: 0.8448 (tpp) cc_final: 0.7959 (mmm) REVERT: F 198 LYS cc_start: 0.8952 (tppt) cc_final: 0.8643 (tppt) REVERT: F 210 MET cc_start: 0.9221 (tpp) cc_final: 0.8981 (tpp) REVERT: F 348 MET cc_start: 0.9226 (mtt) cc_final: 0.8896 (ptp) REVERT: G 198 LYS cc_start: 0.9015 (tppt) cc_final: 0.8804 (tppt) REVERT: G 210 MET cc_start: 0.9303 (tpp) cc_final: 0.8879 (tpp) REVERT: G 234 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8492 (mpp) REVERT: G 410 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8491 (m-90) REVERT: G 531 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.7280 (tptt) outliers start: 208 outliers final: 107 residues processed: 388 average time/residue: 0.3637 time to fit residues: 226.9511 Evaluate side-chains 308 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 178 time to evaluate : 3.187 ------------------------------------------------------------------------------- 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 64 GLN Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 1 MET 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 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 180 ILE Chi-restraints excluded: chain A residue 192 ASP 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 262 GLN 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 373 SER 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 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 205 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 262 GLN Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 VAL 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 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 205 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 248 VAL 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 373 SER Chi-restraints excluded: chain C residue 393 LEU 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 444 LEU Chi-restraints excluded: chain C residue 459 ILE 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 285 CYS 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 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 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 360 LEU 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 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 179 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 367 THR 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 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS 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 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 263 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 165 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 318 optimal weight: 2.9990 chunk 59 optimal weight: 50.0000 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN B 225 HIS C 262 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 536 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053318 restraints weight = 155796.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052394 restraints weight = 140390.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052327 restraints weight = 96790.836| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27854 Z= 0.123 Angle : 0.697 12.251 37676 Z= 0.333 Chirality : 0.041 0.173 4337 Planarity : 0.005 0.066 4780 Dihedral : 11.722 117.184 3991 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 4.84 % Allowed : 25.36 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3328 helix: 0.11 (0.12), residues: 1940 sheet: -0.69 (0.28), residues: 259 loop : -1.10 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 260 HIS 0.013 0.001 HIS B 225 PHE 0.013 0.001 PHE F 532 TYR 0.019 0.001 TYR D 305 ARG 0.007 0.000 ARG I 59 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1085) hydrogen bonds : angle 4.45400 ( 3153) covalent geometry : bond 0.00288 (27854) covalent geometry : angle 0.69730 (37676) *********************** 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 338 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 189 time to evaluate : 3.609 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 68 LEU cc_start: 0.5769 (pt) cc_final: 0.5457 (pp) REVERT: M 47 MET cc_start: 0.6945 (mmm) cc_final: 0.5945 (tmm) REVERT: A 128 MET cc_start: 0.9155 (mmm) cc_final: 0.8699 (mtm) REVERT: A 206 ASP cc_start: 0.9069 (m-30) cc_final: 0.8728 (m-30) REVERT: A 212 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8796 (ttpt) REVERT: A 372 LYS cc_start: 0.8784 (mtpm) cc_final: 0.8446 (tptp) REVERT: A 399 MET cc_start: 0.8430 (tpp) cc_final: 0.8081 (mmm) REVERT: B 114 MET cc_start: 0.8684 (pmm) cc_final: 0.8368 (pmm) REVERT: B 210 MET cc_start: 0.9003 (tpp) cc_final: 0.8665 (tpp) REVERT: B 262 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8894 (pp30) REVERT: B 307 MET cc_start: 0.8918 (mmm) cc_final: 0.8518 (mmm) REVERT: B 410 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.8597 (m-90) REVERT: B 449 MET cc_start: 0.8610 (pmm) cc_final: 0.8197 (pmm) REVERT: C 218 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (pt) REVERT: C 234 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8670 (mtm) REVERT: C 307 MET cc_start: 0.8787 (tpp) cc_final: 0.8416 (tpp) REVERT: C 410 TRP cc_start: 0.9128 (OUTLIER) cc_final: 0.8727 (m-90) REVERT: C 444 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 533 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.9012 (tpp) REVERT: D 150 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8840 (mp) REVERT: D 309 MET cc_start: 0.9087 (mmm) cc_final: 0.8859 (mmm) REVERT: D 351 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9457 (mt) REVERT: D 355 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9418 (mm) REVERT: D 410 TRP cc_start: 0.9019 (OUTLIER) cc_final: 0.8544 (m-90) REVERT: E 150 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8766 (tm) REVERT: E 399 MET cc_start: 0.8438 (tpp) cc_final: 0.8021 (mmm) REVERT: F 147 MET cc_start: 0.8621 (mtp) cc_final: 0.8355 (ptm) REVERT: F 198 LYS cc_start: 0.8978 (tppt) cc_final: 0.8681 (tppt) REVERT: F 210 MET cc_start: 0.9202 (tpp) cc_final: 0.8972 (tpp) REVERT: F 399 MET cc_start: 0.8914 (tpp) cc_final: 0.8474 (mmm) REVERT: F 410 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8610 (m-90) REVERT: G 210 MET cc_start: 0.9273 (tpp) cc_final: 0.8923 (tpp) REVERT: G 316 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: G 410 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.8545 (m-90) REVERT: G 531 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.7588 (tptt) outliers start: 149 outliers final: 94 residues processed: 325 average time/residue: 0.3795 time to fit residues: 199.8825 Evaluate side-chains 289 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 178 time to evaluate : 3.305 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR 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 192 ASP Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 227 THR 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 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 155 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 GLN 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 410 TRP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 144 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 218 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 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 410 TRP 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 240 ILE Chi-restraints excluded: chain D residue 285 CYS 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 351 LEU Chi-restraints excluded: chain D residue 355 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 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 F residue 115 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 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 393 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 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 113 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 229 optimal weight: 10.0000 chunk 332 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 43 optimal weight: 50.0000 chunk 50 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 50.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 HIS J 19 HIS C 262 GLN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050260 restraints weight = 150352.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048829 restraints weight = 140863.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046487 restraints weight = 128290.347| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27854 Z= 0.153 Angle : 0.691 12.183 37676 Z= 0.332 Chirality : 0.041 0.173 4337 Planarity : 0.005 0.065 4780 Dihedral : 11.317 115.893 3973 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 4.90 % Allowed : 25.55 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3328 helix: 0.32 (0.13), residues: 1930 sheet: -0.50 (0.29), residues: 259 loop : -1.03 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 410 HIS 0.012 0.001 HIS A 225 PHE 0.016 0.001 PHE B 204 TYR 0.028 0.001 TYR C 305 ARG 0.009 0.000 ARG J 62 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1085) hydrogen bonds : angle 4.40557 ( 3153) covalent geometry : bond 0.00354 (27854) covalent geometry : angle 0.69115 (37676) *********************** 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 341 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 190 time to evaluate : 3.533 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: L 47 MET cc_start: 0.3073 (mmt) cc_final: 0.1957 (tmm) REVERT: M 47 MET cc_start: 0.7188 (mmm) cc_final: 0.6335 (tmm) REVERT: A 128 MET cc_start: 0.9237 (mmm) cc_final: 0.8526 (mtm) REVERT: A 206 ASP cc_start: 0.9114 (m-30) cc_final: 0.8780 (m-30) REVERT: A 212 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (ttpt) REVERT: A 399 MET cc_start: 0.8319 (tpp) cc_final: 0.7889 (mmm) REVERT: B 128 MET cc_start: 0.9139 (mmm) cc_final: 0.8912 (mmm) REVERT: B 210 MET cc_start: 0.9044 (tpp) cc_final: 0.8697 (tpp) REVERT: B 262 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8883 (pp30) REVERT: B 348 MET cc_start: 0.9435 (ppp) cc_final: 0.9109 (ppp) REVERT: B 410 TRP cc_start: 0.9115 (OUTLIER) cc_final: 0.8640 (m-90) REVERT: C 114 MET cc_start: 0.8688 (pmm) cc_final: 0.8480 (pmm) REVERT: C 234 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8580 (mtm) REVERT: C 307 MET cc_start: 0.8871 (tpp) cc_final: 0.8466 (tpp) REVERT: C 444 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8868 (mm) REVERT: D 150 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9023 (mm) REVERT: D 355 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9419 (mm) REVERT: D 393 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9424 (pp) REVERT: D 410 TRP cc_start: 0.9026 (OUTLIER) cc_final: 0.8546 (m-90) REVERT: E 150 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8818 (tm) REVERT: E 399 MET cc_start: 0.8505 (tpp) cc_final: 0.8225 (mmm) REVERT: F 147 MET cc_start: 0.8747 (mtp) cc_final: 0.8448 (ptp) REVERT: F 198 LYS cc_start: 0.8946 (tppt) cc_final: 0.8621 (tppt) REVERT: F 210 MET cc_start: 0.9187 (tpp) cc_final: 0.8945 (tpp) REVERT: F 348 MET cc_start: 0.9247 (mtt) cc_final: 0.9009 (ptp) REVERT: F 399 MET cc_start: 0.8961 (tpp) cc_final: 0.8530 (mmm) REVERT: F 410 TRP cc_start: 0.9192 (OUTLIER) cc_final: 0.8659 (m-90) REVERT: G 128 MET cc_start: 0.9329 (mmm) cc_final: 0.8602 (mtt) REVERT: G 234 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8444 (mpp) REVERT: G 410 TRP cc_start: 0.8898 (OUTLIER) cc_final: 0.8495 (m-90) REVERT: G 531 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.7595 (tptt) outliers start: 151 outliers final: 98 residues processed: 326 average time/residue: 0.3767 time to fit residues: 198.8643 Evaluate side-chains 294 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 182 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR 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 192 ASP Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 227 THR 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 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 155 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 GLN 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 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 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 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 459 ILE 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 240 ILE Chi-restraints excluded: chain D residue 285 CYS 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 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 355 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 F residue 115 LEU Chi-restraints excluded: chain F residue 139 ARG 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 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 115 LEU 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 234 MET Chi-restraints excluded: chain G residue 290 VAL 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 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 438 SER Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 93 optimal weight: 0.0870 chunk 158 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 56 ASN J 64 GLN B 350 GLN C 262 GLN ** 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 = 0.3644 r_free = 0.3644 target = 0.082643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052637 restraints weight = 168596.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052091 restraints weight = 136492.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052144 restraints weight = 98661.233| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27854 Z= 0.127 Angle : 0.697 13.564 37676 Z= 0.330 Chirality : 0.041 0.208 4337 Planarity : 0.005 0.064 4780 Dihedral : 10.948 115.768 3959 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 4.22 % Allowed : 26.14 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3328 helix: 0.38 (0.13), residues: 1942 sheet: -0.42 (0.29), residues: 259 loop : -0.93 (0.20), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 410 HIS 0.013 0.001 HIS A 225 PHE 0.016 0.001 PHE F 204 TYR 0.030 0.001 TYR C 305 ARG 0.013 0.000 ARG J 62 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 1085) hydrogen bonds : angle 4.29609 ( 3153) covalent geometry : bond 0.00298 (27854) covalent geometry : angle 0.69737 (37676) *********************** 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 318 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 188 time to evaluate : 3.200 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: H 2 LEU cc_start: -0.3885 (mp) cc_final: -0.4275 (mp) REVERT: H 62 ARG cc_start: 0.5608 (ptm160) cc_final: 0.5342 (ptm160) REVERT: H 68 LEU cc_start: 0.3779 (pt) cc_final: 0.3530 (mt) REVERT: J 62 ARG cc_start: 0.6480 (ttp80) cc_final: 0.5702 (mtp180) REVERT: K 47 MET cc_start: 0.6298 (mmm) cc_final: 0.5435 (ptm) REVERT: L 47 MET cc_start: 0.2871 (mmt) cc_final: 0.1721 (tmm) REVERT: M 47 MET cc_start: 0.7191 (mmm) cc_final: 0.6336 (tmm) REVERT: A 128 MET cc_start: 0.9099 (mmm) cc_final: 0.8516 (mtm) REVERT: A 206 ASP cc_start: 0.9022 (m-30) cc_final: 0.8676 (m-30) REVERT: A 212 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8763 (ttpt) REVERT: A 335 MET cc_start: 0.9034 (mtm) cc_final: 0.8791 (mtt) REVERT: A 372 LYS cc_start: 0.8645 (mtpm) cc_final: 0.8386 (tptp) REVERT: A 399 MET cc_start: 0.8249 (tpp) cc_final: 0.7848 (mmm) REVERT: A 462 MET cc_start: 0.9127 (mtp) cc_final: 0.8288 (ttm) REVERT: B 128 MET cc_start: 0.9179 (mmm) cc_final: 0.8922 (mmm) REVERT: B 210 MET cc_start: 0.9049 (tpp) cc_final: 0.8700 (tpp) REVERT: B 262 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8903 (pp30) REVERT: B 307 MET cc_start: 0.8609 (mmm) cc_final: 0.8266 (mmm) REVERT: B 348 MET cc_start: 0.9307 (ppp) cc_final: 0.9024 (ppp) REVERT: B 410 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.8618 (m-90) REVERT: C 114 MET cc_start: 0.8625 (pmm) cc_final: 0.8346 (pmm) REVERT: C 234 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8619 (mtm) REVERT: C 307 MET cc_start: 0.8818 (tpp) cc_final: 0.8225 (tpp) REVERT: C 444 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8836 (mm) REVERT: D 150 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8822 (mp) REVERT: D 307 MET cc_start: 0.8754 (tpt) cc_final: 0.8481 (mmm) REVERT: D 355 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9398 (mm) REVERT: D 393 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9426 (pp) REVERT: D 410 TRP cc_start: 0.8969 (OUTLIER) cc_final: 0.8538 (m-90) REVERT: E 150 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8880 (tm) REVERT: E 399 MET cc_start: 0.8494 (tpp) cc_final: 0.8043 (mmm) REVERT: F 147 MET cc_start: 0.8645 (mtp) cc_final: 0.8399 (ptp) REVERT: F 210 MET cc_start: 0.9152 (tpp) cc_final: 0.8903 (tpp) REVERT: F 348 MET cc_start: 0.9094 (mtt) cc_final: 0.8783 (ptp) REVERT: F 399 MET cc_start: 0.8989 (tpp) cc_final: 0.8643 (mmm) REVERT: F 410 TRP cc_start: 0.9192 (OUTLIER) cc_final: 0.8584 (m-90) REVERT: G 128 MET cc_start: 0.9348 (mmm) cc_final: 0.8670 (mtt) REVERT: G 234 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8440 (mpp) REVERT: G 316 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: G 371 TYR cc_start: 0.9278 (m-80) cc_final: 0.9055 (m-80) REVERT: G 379 GLN cc_start: 0.9587 (OUTLIER) cc_final: 0.9279 (tm-30) REVERT: G 410 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8495 (m-90) REVERT: G 531 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.7564 (tptt) outliers start: 130 outliers final: 92 residues processed: 306 average time/residue: 0.3795 time to fit residues: 185.8237 Evaluate side-chains 290 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 182 time to evaluate : 2.969 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain I residue 2 LEU 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 105 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET 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 192 ASP Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 227 THR 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 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 155 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 GLN 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 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 234 MET 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 373 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 459 ILE 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 240 ILE Chi-restraints excluded: chain D residue 285 CYS 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 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 242 ARG 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 115 LEU Chi-restraints excluded: chain F residue 139 ARG 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 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 115 LEU 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 234 MET 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 379 GLN 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 531 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 143 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 46 optimal weight: 0.0980 chunk 119 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 229 optimal weight: 0.4980 chunk 17 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN B 237 ASN C 262 GLN F 534 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.082286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047037 restraints weight = 154297.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046632 restraints weight = 129738.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046686 restraints weight = 123809.752| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.7442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27854 Z= 0.181 Angle : 0.717 14.057 37676 Z= 0.344 Chirality : 0.041 0.185 4337 Planarity : 0.005 0.065 4780 Dihedral : 10.728 115.308 3954 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 4.16 % Allowed : 26.17 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3328 helix: 0.55 (0.13), residues: 1962 sheet: -0.29 (0.30), residues: 259 loop : -1.01 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 410 HIS 0.014 0.001 HIS A 225 PHE 0.017 0.001 PHE F 532 TYR 0.034 0.002 TYR C 305 ARG 0.012 0.000 ARG J 63 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 1085) hydrogen bonds : angle 4.39765 ( 3153) covalent geometry : bond 0.00414 (27854) covalent geometry : angle 0.71699 (37676) *********************** 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 318 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 190 time to evaluate : 3.106 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: 0.6371 (mmm) cc_final: 0.5511 (ptm) REVERT: L 47 MET cc_start: 0.2976 (mmt) cc_final: 0.1810 (tmm) REVERT: A 128 MET cc_start: 0.9201 (mmm) cc_final: 0.8675 (mtt) REVERT: A 206 ASP cc_start: 0.9112 (m-30) cc_final: 0.8747 (m-30) REVERT: A 212 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8751 (ttpt) REVERT: A 335 MET cc_start: 0.9063 (mtm) cc_final: 0.8841 (mtt) REVERT: A 399 MET cc_start: 0.8433 (tpp) cc_final: 0.8022 (mmm) REVERT: B 262 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8880 (pp30) REVERT: B 348 MET cc_start: 0.9434 (ppp) cc_final: 0.9189 (ppp) REVERT: B 410 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8571 (m-90) REVERT: C 114 MET cc_start: 0.8739 (pmm) cc_final: 0.8472 (pmm) REVERT: C 234 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8640 (mtm) REVERT: C 307 MET cc_start: 0.8761 (tpp) cc_final: 0.8159 (tpp) REVERT: C 444 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8950 (mm) REVERT: D 150 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8954 (mm) REVERT: D 355 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9468 (mm) REVERT: D 393 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9379 (pp) REVERT: D 410 TRP cc_start: 0.9018 (OUTLIER) cc_final: 0.8458 (m-90) REVERT: D 533 MET cc_start: 0.8221 (mmm) cc_final: 0.7953 (mmm) REVERT: E 150 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8910 (tm) REVERT: E 198 LYS cc_start: 0.8718 (tppt) cc_final: 0.8382 (tppt) REVERT: E 399 MET cc_start: 0.8461 (tpp) cc_final: 0.8039 (mmm) REVERT: F 198 LYS cc_start: 0.9386 (mmtm) cc_final: 0.9178 (tppt) REVERT: F 210 MET cc_start: 0.9232 (tpp) cc_final: 0.8937 (tpp) REVERT: F 410 TRP cc_start: 0.9228 (OUTLIER) cc_final: 0.8470 (m-90) REVERT: G 128 MET cc_start: 0.9266 (mmm) cc_final: 0.8715 (mtt) REVERT: G 234 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8494 (mpp) REVERT: G 316 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: G 335 MET cc_start: 0.8856 (mtm) cc_final: 0.8532 (mtt) REVERT: G 379 GLN cc_start: 0.9625 (OUTLIER) cc_final: 0.9277 (tm-30) REVERT: G 410 TRP cc_start: 0.8958 (OUTLIER) cc_final: 0.8425 (m-90) outliers start: 128 outliers final: 100 residues processed: 307 average time/residue: 0.3681 time to fit residues: 181.9360 Evaluate side-chains 301 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 186 time to evaluate : 3.100 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR 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 192 ASP Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 227 THR 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 155 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 GLN 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 366 ILE 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 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 373 SER Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 459 ILE 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 155 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 285 CYS 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 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 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 115 LEU Chi-restraints excluded: chain F residue 139 ARG 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 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 167 VAL Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET 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 379 GLN 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 438 SER Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.0170 chunk 136 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 chunk 286 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 178 optimal weight: 0.0040 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN A 225 HIS B 283 GLN C 262 GLN C 475 ASN D 482 GLN F 352 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052712 restraints weight = 162396.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.050078 restraints weight = 130867.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050133 restraints weight = 96812.138| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27854 Z= 0.117 Angle : 0.726 14.732 37676 Z= 0.338 Chirality : 0.041 0.241 4337 Planarity : 0.005 0.065 4780 Dihedral : 10.423 115.403 3947 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 3.67 % Allowed : 26.88 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3328 helix: 0.64 (0.13), residues: 1963 sheet: -0.28 (0.29), residues: 259 loop : -0.89 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 410 HIS 0.013 0.001 HIS A 225 PHE 0.023 0.001 PHE F 204 TYR 0.032 0.001 TYR C 305 ARG 0.021 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 1085) hydrogen bonds : angle 4.20694 ( 3153) covalent geometry : bond 0.00275 (27854) covalent geometry : angle 0.72577 (37676) *********************** 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 310 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 197 time to evaluate : 3.489 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: J 62 ARG cc_start: 0.6442 (ttp80) cc_final: 0.5515 (mtp180) REVERT: K 47 MET cc_start: 0.6398 (mmm) cc_final: 0.5564 (ptm) REVERT: L 47 MET cc_start: 0.3030 (mmt) cc_final: 0.1975 (tmm) REVERT: L 77 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.7030 (p90) REVERT: A 128 MET cc_start: 0.9132 (mmm) cc_final: 0.8806 (mtm) REVERT: A 206 ASP cc_start: 0.9089 (m-30) cc_final: 0.8713 (m-30) REVERT: A 212 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8737 (ttpt) REVERT: A 399 MET cc_start: 0.8431 (tpp) cc_final: 0.8069 (mmm) REVERT: A 462 MET cc_start: 0.9145 (mtp) cc_final: 0.8260 (ttm) REVERT: B 128 MET cc_start: 0.9209 (mmm) cc_final: 0.8414 (mtp) REVERT: B 210 MET cc_start: 0.9077 (tpp) cc_final: 0.8700 (tpp) REVERT: B 262 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8890 (pp30) REVERT: B 307 MET cc_start: 0.8543 (mmm) cc_final: 0.7991 (mmm) REVERT: B 348 MET cc_start: 0.9344 (ppp) cc_final: 0.9095 (ppp) REVERT: B 410 TRP cc_start: 0.8941 (OUTLIER) cc_final: 0.8685 (m-90) REVERT: C 234 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8784 (mtm) REVERT: C 307 MET cc_start: 0.8688 (tpp) cc_final: 0.8320 (tpp) REVERT: C 393 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9509 (pp) REVERT: C 439 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9134 (tppp) REVERT: C 444 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8874 (mm) REVERT: D 150 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8919 (mm) REVERT: D 309 MET cc_start: 0.8990 (mmm) cc_final: 0.8644 (mmm) REVERT: D 355 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9429 (mm) REVERT: D 393 LEU cc_start: 0.9730 (tt) cc_final: 0.9496 (pp) REVERT: D 410 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.8608 (m-90) REVERT: E 150 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8861 (tm) REVERT: E 198 LYS cc_start: 0.8731 (tppt) cc_final: 0.8370 (tppt) REVERT: E 399 MET cc_start: 0.8498 (tpp) cc_final: 0.8030 (mmm) REVERT: F 114 MET cc_start: 0.8656 (pmm) cc_final: 0.8209 (pmm) REVERT: F 147 MET cc_start: 0.8888 (mtp) cc_final: 0.8654 (ptm) REVERT: F 348 MET cc_start: 0.9292 (mtt) cc_final: 0.9081 (ptp) REVERT: F 410 TRP cc_start: 0.9117 (OUTLIER) cc_final: 0.8573 (m-90) REVERT: G 128 MET cc_start: 0.9278 (mmm) cc_final: 0.8881 (mtt) REVERT: G 379 GLN cc_start: 0.9552 (OUTLIER) cc_final: 0.9257 (tm-30) REVERT: G 410 TRP cc_start: 0.8802 (OUTLIER) cc_final: 0.8460 (m-90) REVERT: G 531 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.7792 (tptt) outliers start: 113 outliers final: 81 residues processed: 301 average time/residue: 0.3761 time to fit residues: 183.0094 Evaluate side-chains 284 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 187 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR 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 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 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 155 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 383 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 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 316 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 393 LEU 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 D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 316 GLU 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 460 ILE 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 F residue 139 ARG Chi-restraints excluded: chain F residue 155 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 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 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 379 GLN 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 438 SER Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 224 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 256 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 50.0000 chunk 163 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 160 optimal weight: 0.0470 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.083636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051389 restraints weight = 161398.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050925 restraints weight = 127945.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050873 restraints weight = 113913.055| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.7754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27854 Z= 0.117 Angle : 0.741 13.192 37676 Z= 0.344 Chirality : 0.041 0.198 4337 Planarity : 0.005 0.066 4780 Dihedral : 10.079 113.943 3940 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 3.21 % Allowed : 27.24 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3328 helix: 0.71 (0.13), residues: 1928 sheet: -0.18 (0.29), residues: 259 loop : -0.87 (0.20), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 410 HIS 0.019 0.001 HIS A 225 PHE 0.017 0.001 PHE L 75 TYR 0.038 0.001 TYR J 77 ARG 0.013 0.000 ARG J 62 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 1085) hydrogen bonds : angle 4.17748 ( 3153) covalent geometry : bond 0.00274 (27854) covalent geometry : angle 0.74064 (37676) ********************** 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 292 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 193 time to evaluate : 3.162 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: J 8 ARG cc_start: 0.1593 (mtt180) cc_final: 0.1171 (mtt180) REVERT: J 16 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7456 (ptp90) REVERT: K 47 MET cc_start: 0.6434 (mmm) cc_final: 0.5594 (ptm) REVERT: L 47 MET cc_start: 0.3097 (mmt) cc_final: 0.2023 (tmm) REVERT: A 128 MET cc_start: 0.9232 (mmm) cc_final: 0.8633 (mtm) REVERT: A 147 MET cc_start: 0.8901 (mmp) cc_final: 0.8683 (mmp) REVERT: A 206 ASP cc_start: 0.9139 (m-30) cc_final: 0.8769 (m-30) REVERT: A 212 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8678 (ttpt) REVERT: A 372 LYS cc_start: 0.8991 (mtpm) cc_final: 0.8665 (tptp) REVERT: A 399 MET cc_start: 0.8536 (tpp) cc_final: 0.8052 (mmm) REVERT: B 128 MET cc_start: 0.9244 (mmm) cc_final: 0.8237 (mtp) REVERT: B 210 MET cc_start: 0.9054 (tpp) cc_final: 0.8655 (tpp) REVERT: B 262 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8863 (pp30) REVERT: B 348 MET cc_start: 0.9429 (ppp) cc_final: 0.9182 (ppp) REVERT: B 399 MET cc_start: 0.8092 (mmm) cc_final: 0.7874 (mmm) REVERT: B 410 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8771 (m-90) REVERT: C 234 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: C 307 MET cc_start: 0.8771 (tpp) cc_final: 0.8259 (tpp) REVERT: C 444 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8642 (mm) REVERT: D 150 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8851 (mm) REVERT: D 309 MET cc_start: 0.9025 (mmm) cc_final: 0.8697 (mmm) REVERT: D 316 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: D 355 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9419 (mm) REVERT: D 393 LEU cc_start: 0.9590 (tt) cc_final: 0.9365 (pp) REVERT: D 410 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8544 (m-90) REVERT: E 150 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8830 (tm) REVERT: E 198 LYS cc_start: 0.8684 (tppt) cc_final: 0.8319 (tppt) REVERT: E 399 MET cc_start: 0.8510 (tpp) cc_final: 0.7994 (mmm) REVERT: F 114 MET cc_start: 0.8652 (pmm) cc_final: 0.8278 (pmm) REVERT: F 348 MET cc_start: 0.9264 (mtt) cc_final: 0.9057 (ptp) REVERT: F 410 TRP cc_start: 0.9142 (OUTLIER) cc_final: 0.8515 (m-90) REVERT: G 128 MET cc_start: 0.9226 (mmm) cc_final: 0.8611 (mtt) REVERT: G 216 ASP cc_start: 0.9200 (m-30) cc_final: 0.8672 (t0) REVERT: G 348 MET cc_start: 0.9309 (ptp) cc_final: 0.8863 (ptp) REVERT: G 379 GLN cc_start: 0.9574 (OUTLIER) cc_final: 0.9289 (tm-30) REVERT: G 410 TRP cc_start: 0.8880 (OUTLIER) cc_final: 0.8468 (m-90) REVERT: G 531 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8038 (tptt) outliers start: 99 outliers final: 72 residues processed: 283 average time/residue: 0.3687 time to fit residues: 170.3773 Evaluate side-chains 277 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 190 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR 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 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 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 155 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 383 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 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 373 SER 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 240 ILE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 316 GLU 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 460 ILE 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 F residue 139 ARG 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 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 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 379 GLN 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 438 SER Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 216 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 125 optimal weight: 0.2980 chunk 325 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** J 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN A 534 GLN B 350 GLN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN F 352 ASN ** G 158 HIS ** 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 = 0.3602 r_free = 0.3602 target = 0.081716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050278 restraints weight = 164397.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049895 restraints weight = 133605.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049717 restraints weight = 116004.293| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27854 Z= 0.199 Angle : 0.769 13.117 37676 Z= 0.367 Chirality : 0.041 0.230 4337 Planarity : 0.005 0.064 4780 Dihedral : 9.931 112.234 3937 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 2.99 % Allowed : 27.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3328 helix: 0.68 (0.13), residues: 1938 sheet: -0.08 (0.30), residues: 259 loop : -0.88 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 410 HIS 0.011 0.001 HIS A 225 PHE 0.019 0.001 PHE F 204 TYR 0.041 0.002 TYR B 540 ARG 0.011 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1085) hydrogen bonds : angle 4.43866 ( 3153) covalent geometry : bond 0.00448 (27854) covalent geometry : angle 0.76916 (37676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11782.48 seconds wall clock time: 205 minutes 38.00 seconds (12338.00 seconds total)