Starting phenix.real_space_refine on Fri Mar 6 10:22:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6riq_4897/03_2026/6riq_4897_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6riq_4897/03_2026/6riq_4897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6riq_4897/03_2026/6riq_4897_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6riq_4897/03_2026/6riq_4897_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6riq_4897/03_2026/6riq_4897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6riq_4897/03_2026/6riq_4897.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 11 5.21 5 S 110 5.16 5 C 18942 2.51 5 N 5368 2.21 5 O 5863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 286 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30327 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "J" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "K" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "N" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "O" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "P" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "Q" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "R" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "S" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "T" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 784 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "V" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1941 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} 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: "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} Chain: "J" 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: "K" 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: "M" 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: "N" 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: "Q" 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: "R" 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: "U" 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: "V" 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: 7.20, per 1000 atoms: 0.24 Number of scatterers: 30327 At special positions: 0 Unit cell: (110.818, 116.607, 194.345, 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 110 16.00 P 33 15.00 Mg 11 11.99 O 5863 8.00 N 5368 7.00 C 18942 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7216 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 33 sheets defined 36.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.863A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.970A pdb=" N ARG B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 31 removed outlier: 3.615A pdb=" N ALA C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.788A pdb=" N ILE C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 66 removed outlier: 3.558A pdb=" N VAL C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.939A pdb=" N LEU C 97 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.538A pdb=" N VAL C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.758A pdb=" N ALA C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.865A pdb=" N MET C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.855A pdb=" N THR C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 removed outlier: 3.668A pdb=" N VAL C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 removed outlier: 4.394A pdb=" N LEU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.737A pdb=" N GLN C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 31 removed outlier: 3.526A pdb=" N ALA D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 removed outlier: 3.640A pdb=" N ILE D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.947A pdb=" N LEU D 97 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.541A pdb=" N LYS D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 removed outlier: 3.828A pdb=" N ALA D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 157 removed outlier: 3.566A pdb=" N MET D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 removed outlier: 3.597A pdb=" N VAL D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 222 removed outlier: 4.477A pdb=" N LEU D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.722A pdb=" N GLN D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.863A pdb=" N ARG E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.970A pdb=" N ARG F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER F 242 " --> pdb=" O ASP F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 31 removed outlier: 3.616A pdb=" N ALA G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 50 removed outlier: 3.788A pdb=" N ILE G 49 " --> pdb=" O ASN G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 66 removed outlier: 3.558A pdb=" N VAL G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.941A pdb=" N LEU G 97 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 113 removed outlier: 3.537A pdb=" N VAL G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.758A pdb=" N ALA G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 157 removed outlier: 3.865A pdb=" N MET G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.855A pdb=" N THR G 188 " --> pdb=" O PRO G 184 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 202 removed outlier: 3.668A pdb=" N VAL G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 222 removed outlier: 4.394A pdb=" N LEU G 217 " --> pdb=" O SER G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 229 Processing helix chain 'G' and resid 232 through 246 removed outlier: 3.737A pdb=" N GLN G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 242 removed outlier: 3.863A pdb=" N ARG H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER H 242 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 242 removed outlier: 3.970A pdb=" N ARG I 241 " --> pdb=" O GLU I 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER I 242 " --> pdb=" O ASP I 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 31 removed outlier: 3.615A pdb=" N ALA J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY J 31 " --> pdb=" O LEU J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.788A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 66 removed outlier: 3.559A pdb=" N VAL J 63 " --> pdb=" O ASP J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 93 through 97 removed outlier: 3.939A pdb=" N LEU J 97 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 113 removed outlier: 3.537A pdb=" N VAL J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 removed outlier: 3.758A pdb=" N ALA J 131 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE J 134 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 157 removed outlier: 3.865A pdb=" N MET J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 189 removed outlier: 3.855A pdb=" N THR J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 202 removed outlier: 3.668A pdb=" N VAL J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 222 removed outlier: 4.394A pdb=" N LEU J 217 " --> pdb=" O SER J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 229 Processing helix chain 'J' and resid 232 through 246 removed outlier: 3.739A pdb=" N GLN J 236 " --> pdb=" O SER J 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA J 241 " --> pdb=" O ALA J 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 242 " --> pdb=" O TYR J 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP J 243 " --> pdb=" O SER J 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 31 removed outlier: 3.525A pdb=" N ALA K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.639A pdb=" N ILE K 49 " --> pdb=" O ASN K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 66 Processing helix chain 'K' and resid 69 through 74 Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.946A pdb=" N LEU K 97 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 113 removed outlier: 3.540A pdb=" N LYS K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 134 removed outlier: 3.829A pdb=" N ALA K 131 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE K 134 " --> pdb=" O LEU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 157 removed outlier: 3.567A pdb=" N MET K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 202 removed outlier: 3.597A pdb=" N VAL K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 222 removed outlier: 4.477A pdb=" N LEU K 217 " --> pdb=" O SER K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 229 Processing helix chain 'K' and resid 232 through 246 removed outlier: 3.721A pdb=" N GLN K 236 " --> pdb=" O SER K 232 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K 241 " --> pdb=" O ALA K 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP K 243 " --> pdb=" O SER K 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 242 removed outlier: 3.970A pdb=" N ARG L 241 " --> pdb=" O GLU L 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER L 242 " --> pdb=" O ASP L 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 31 removed outlier: 3.615A pdb=" N ALA M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY M 31 " --> pdb=" O LEU M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 50 removed outlier: 3.789A pdb=" N ILE M 49 " --> pdb=" O ASN M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 66 removed outlier: 3.558A pdb=" N VAL M 63 " --> pdb=" O ASP M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 74 Processing helix chain 'M' and resid 93 through 97 removed outlier: 3.940A pdb=" N LEU M 97 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 113 removed outlier: 3.537A pdb=" N VAL M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP M 112 " --> pdb=" O GLU M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 134 removed outlier: 3.759A pdb=" N ALA M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE M 134 " --> pdb=" O LEU M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 157 removed outlier: 3.865A pdb=" N MET M 155 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 189 removed outlier: 3.855A pdb=" N THR M 188 " --> pdb=" O PRO M 184 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 189 " --> pdb=" O GLU M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 202 removed outlier: 3.668A pdb=" N VAL M 198 " --> pdb=" O SER M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 222 removed outlier: 4.394A pdb=" N LEU M 217 " --> pdb=" O SER M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 229 Processing helix chain 'M' and resid 232 through 246 removed outlier: 3.738A pdb=" N GLN M 236 " --> pdb=" O SER M 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA M 241 " --> pdb=" O ALA M 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL M 242 " --> pdb=" O TYR M 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP M 243 " --> pdb=" O SER M 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 31 removed outlier: 3.526A pdb=" N ALA N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 50 removed outlier: 3.638A pdb=" N ILE N 49 " --> pdb=" O ASN N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 66 Processing helix chain 'N' and resid 69 through 74 Processing helix chain 'N' and resid 93 through 97 removed outlier: 3.946A pdb=" N LEU N 97 " --> pdb=" O LYS N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 113 removed outlier: 3.540A pdb=" N LYS N 111 " --> pdb=" O ALA N 107 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 134 removed outlier: 3.828A pdb=" N ALA N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 157 removed outlier: 3.566A pdb=" N MET N 155 " --> pdb=" O ASP N 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY N 157 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 202 removed outlier: 3.597A pdb=" N VAL N 198 " --> pdb=" O SER N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 222 removed outlier: 4.477A pdb=" N LEU N 217 " --> pdb=" O SER N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 229 Processing helix chain 'N' and resid 232 through 246 removed outlier: 3.722A pdb=" N GLN N 236 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA N 241 " --> pdb=" O ALA N 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP N 243 " --> pdb=" O SER N 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 242 removed outlier: 3.863A pdb=" N ARG O 241 " --> pdb=" O GLU O 237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER O 242 " --> pdb=" O ASP O 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 242 removed outlier: 3.970A pdb=" N ARG P 241 " --> pdb=" O GLU P 237 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER P 242 " --> pdb=" O ASP P 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 31 removed outlier: 3.616A pdb=" N ALA Q 28 " --> pdb=" O GLY Q 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY Q 31 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 50 removed outlier: 3.788A pdb=" N ILE Q 49 " --> pdb=" O ASN Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 66 removed outlier: 3.558A pdb=" N VAL Q 63 " --> pdb=" O ASP Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 93 through 97 removed outlier: 3.940A pdb=" N LEU Q 97 " --> pdb=" O LYS Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 113 removed outlier: 3.537A pdb=" N VAL Q 105 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 134 removed outlier: 3.758A pdb=" N ALA Q 131 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE Q 134 " --> pdb=" O LEU Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 157 removed outlier: 3.865A pdb=" N MET Q 155 " --> pdb=" O ASP Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 189 removed outlier: 3.855A pdb=" N THR Q 188 " --> pdb=" O PRO Q 184 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Q 189 " --> pdb=" O GLU Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 202 removed outlier: 3.669A pdb=" N VAL Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 222 removed outlier: 4.394A pdb=" N LEU Q 217 " --> pdb=" O SER Q 213 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 229 Processing helix chain 'Q' and resid 232 through 246 removed outlier: 3.738A pdb=" N GLN Q 236 " --> pdb=" O SER Q 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL Q 242 " --> pdb=" O TYR Q 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP Q 243 " --> pdb=" O SER Q 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 31 removed outlier: 3.525A pdb=" N ALA R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 50 removed outlier: 3.639A pdb=" N ILE R 49 " --> pdb=" O ASN R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 66 Processing helix chain 'R' and resid 69 through 74 Processing helix chain 'R' and resid 93 through 97 removed outlier: 3.946A pdb=" N LEU R 97 " --> pdb=" O LYS R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 113 removed outlier: 3.541A pdb=" N LYS R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP R 112 " --> pdb=" O GLU R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 134 removed outlier: 3.828A pdb=" N ALA R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 157 removed outlier: 3.565A pdb=" N MET R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY R 157 " --> pdb=" O ASP R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 202 removed outlier: 3.597A pdb=" N VAL R 198 " --> pdb=" O SER R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 222 removed outlier: 4.477A pdb=" N LEU R 217 " --> pdb=" O SER R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 229 Processing helix chain 'R' and resid 232 through 246 removed outlier: 3.721A pdb=" N GLN R 236 " --> pdb=" O SER R 232 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 242 removed outlier: 3.863A pdb=" N ARG S 241 " --> pdb=" O GLU S 237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER S 242 " --> pdb=" O ASP S 238 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 242 removed outlier: 3.970A pdb=" N ARG T 241 " --> pdb=" O GLU T 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER T 242 " --> pdb=" O ASP T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 31 removed outlier: 3.615A pdb=" N ALA U 28 " --> pdb=" O GLY U 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY U 31 " --> pdb=" O LEU U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 50 removed outlier: 3.788A pdb=" N ILE U 49 " --> pdb=" O ASN U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 66 removed outlier: 3.558A pdb=" N VAL U 63 " --> pdb=" O ASP U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 74 Processing helix chain 'U' and resid 93 through 97 removed outlier: 3.940A pdb=" N LEU U 97 " --> pdb=" O LYS U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 113 removed outlier: 3.537A pdb=" N VAL U 105 " --> pdb=" O GLY U 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 125 through 134 removed outlier: 3.758A pdb=" N ALA U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 157 removed outlier: 3.865A pdb=" N MET U 155 " --> pdb=" O ASP U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 189 removed outlier: 3.855A pdb=" N THR U 188 " --> pdb=" O PRO U 184 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS U 189 " --> pdb=" O GLU U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 202 removed outlier: 3.668A pdb=" N VAL U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 213 through 222 removed outlier: 4.394A pdb=" N LEU U 217 " --> pdb=" O SER U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 229 Processing helix chain 'U' and resid 232 through 246 removed outlier: 3.738A pdb=" N GLN U 236 " --> pdb=" O SER U 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA U 241 " --> pdb=" O ALA U 237 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL U 242 " --> pdb=" O TYR U 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP U 243 " --> pdb=" O SER U 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 31 removed outlier: 3.525A pdb=" N ALA V 28 " --> pdb=" O GLY V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 50 removed outlier: 3.639A pdb=" N ILE V 49 " --> pdb=" O ASN V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 66 Processing helix chain 'V' and resid 69 through 74 Processing helix chain 'V' and resid 93 through 97 removed outlier: 3.947A pdb=" N LEU V 97 " --> pdb=" O LYS V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 113 removed outlier: 3.540A pdb=" N LYS V 111 " --> pdb=" O ALA V 107 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP V 112 " --> pdb=" O GLU V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 134 removed outlier: 3.828A pdb=" N ALA V 131 " --> pdb=" O GLY V 127 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE V 134 " --> pdb=" O LEU V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 157 removed outlier: 3.566A pdb=" N MET V 155 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY V 157 " --> pdb=" O ASP V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 202 removed outlier: 3.597A pdb=" N VAL V 198 " --> pdb=" O SER V 194 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 222 removed outlier: 4.477A pdb=" N LEU V 217 " --> pdb=" O SER V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 229 Processing helix chain 'V' and resid 232 through 246 removed outlier: 3.721A pdb=" N GLN V 236 " --> pdb=" O SER V 232 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA V 241 " --> pdb=" O ALA V 237 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP V 243 " --> pdb=" O SER V 239 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 removed outlier: 7.305A pdb=" N GLY A 199 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 222 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET A 201 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 172 removed outlier: 5.860A pdb=" N ILE A 170 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 160 removed outlier: 7.326A pdb=" N GLY B 199 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 222 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET B 201 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.060A pdb=" N ILE B 170 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.660A pdb=" N THR C 34 " --> pdb=" O HIS C 84 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 86 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 36 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU C 207 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU C 177 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 209 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 179 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG C 181 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.618A pdb=" N THR D 34 " --> pdb=" O HIS D 84 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU D 86 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 36 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 207 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 177 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 209 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 179 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG D 181 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 158 through 160 removed outlier: 7.306A pdb=" N GLY E 199 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU E 222 " --> pdb=" O GLY E 199 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET E 201 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 172 removed outlier: 5.860A pdb=" N ILE E 170 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 158 through 160 removed outlier: 7.326A pdb=" N GLY F 199 " --> pdb=" O GLN F 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU F 222 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET F 201 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.060A pdb=" N ILE F 170 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.660A pdb=" N THR G 34 " --> pdb=" O HIS G 84 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU G 86 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE G 36 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU G 207 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU G 177 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 209 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU G 179 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG G 181 " --> pdb=" O PRO G 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 158 through 160 removed outlier: 7.306A pdb=" N GLY H 199 " --> pdb=" O GLN H 220 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU H 222 " --> pdb=" O GLY H 199 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET H 201 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 169 through 172 removed outlier: 5.860A pdb=" N ILE H 170 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 158 through 160 removed outlier: 7.326A pdb=" N GLY I 199 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 222 " --> pdb=" O GLY I 199 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N MET I 201 " --> pdb=" O LEU I 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 169 through 172 removed outlier: 6.059A pdb=" N ILE I 170 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU I 189 " --> pdb=" O LEU I 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.660A pdb=" N THR J 34 " --> pdb=" O HIS J 84 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU J 86 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE J 36 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU J 207 " --> pdb=" O GLU J 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU J 177 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL J 209 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU J 179 " --> pdb=" O VAL J 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG J 181 " --> pdb=" O PRO J 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 75 through 76 removed outlier: 6.618A pdb=" N THR K 34 " --> pdb=" O HIS K 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU K 86 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE K 36 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU K 207 " --> pdb=" O GLU K 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU K 177 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL K 209 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU K 179 " --> pdb=" O VAL K 209 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG K 181 " --> pdb=" O PRO K 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 158 through 160 removed outlier: 7.325A pdb=" N GLY L 199 " --> pdb=" O GLN L 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU L 222 " --> pdb=" O GLY L 199 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N MET L 201 " --> pdb=" O LEU L 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 169 through 172 removed outlier: 6.060A pdb=" N ILE L 170 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU L 189 " --> pdb=" O LEU L 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 75 through 76 removed outlier: 6.659A pdb=" N THR M 34 " --> pdb=" O HIS M 84 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU M 86 " --> pdb=" O THR M 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE M 36 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU M 207 " --> pdb=" O GLU M 175 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU M 177 " --> pdb=" O LEU M 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL M 209 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU M 179 " --> pdb=" O VAL M 209 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG M 181 " --> pdb=" O PRO M 211 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 75 through 76 removed outlier: 6.618A pdb=" N THR N 34 " --> pdb=" O HIS N 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU N 86 " --> pdb=" O THR N 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE N 36 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU N 207 " --> pdb=" O GLU N 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU N 177 " --> pdb=" O LEU N 207 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL N 209 " --> pdb=" O LEU N 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU N 179 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG N 181 " --> pdb=" O PRO N 211 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 158 through 160 removed outlier: 7.306A pdb=" N GLY O 199 " --> pdb=" O GLN O 220 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU O 222 " --> pdb=" O GLY O 199 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET O 201 " --> pdb=" O LEU O 222 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 169 through 172 removed outlier: 5.860A pdb=" N ILE O 170 " --> pdb=" O LEU O 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 158 through 160 removed outlier: 7.326A pdb=" N GLY P 199 " --> pdb=" O GLN P 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU P 222 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N MET P 201 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 169 through 172 removed outlier: 6.060A pdb=" N ILE P 170 " --> pdb=" O LEU P 190 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU P 189 " --> pdb=" O LEU P 206 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 75 through 76 removed outlier: 6.660A pdb=" N THR Q 34 " --> pdb=" O HIS Q 84 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU Q 86 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE Q 36 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU Q 207 " --> pdb=" O GLU Q 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU Q 177 " --> pdb=" O LEU Q 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL Q 209 " --> pdb=" O LEU Q 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU Q 179 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG Q 181 " --> pdb=" O PRO Q 211 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 75 through 76 removed outlier: 6.618A pdb=" N THR R 34 " --> pdb=" O HIS R 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU R 86 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE R 36 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU R 207 " --> pdb=" O GLU R 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU R 177 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL R 209 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU R 179 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG R 181 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 158 through 160 removed outlier: 7.306A pdb=" N GLY S 199 " --> pdb=" O GLN S 220 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU S 222 " --> pdb=" O GLY S 199 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET S 201 " --> pdb=" O LEU S 222 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 169 through 172 removed outlier: 5.860A pdb=" N ILE S 170 " --> pdb=" O LEU S 190 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 158 through 160 removed outlier: 7.326A pdb=" N GLY T 199 " --> pdb=" O GLN T 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU T 222 " --> pdb=" O GLY T 199 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N MET T 201 " --> pdb=" O LEU T 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 169 through 172 removed outlier: 6.060A pdb=" N ILE T 170 " --> pdb=" O LEU T 190 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU T 189 " --> pdb=" O LEU T 206 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 75 through 76 removed outlier: 6.659A pdb=" N THR U 34 " --> pdb=" O HIS U 84 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU U 86 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE U 36 " --> pdb=" O LEU U 86 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU U 207 " --> pdb=" O GLU U 175 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU U 177 " --> pdb=" O LEU U 207 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL U 209 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU U 179 " --> pdb=" O VAL U 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG U 181 " --> pdb=" O PRO U 211 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 75 through 76 removed outlier: 6.618A pdb=" N THR V 34 " --> pdb=" O HIS V 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU V 86 " --> pdb=" O THR V 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE V 36 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU V 207 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU V 177 " --> pdb=" O LEU V 207 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL V 209 " --> pdb=" O LEU V 177 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU V 179 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG V 181 " --> pdb=" O PRO V 211 " (cutoff:3.500A) 1197 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10271 1.34 - 1.46: 5541 1.46 - 1.58: 14647 1.58 - 1.70: 55 1.70 - 1.82: 187 Bond restraints: 30701 Sorted by residual: bond pdb=" C4 ATP D 302 " pdb=" C5 ATP D 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.59e+01 bond pdb=" C4 ATP R 302 " pdb=" C5 ATP R 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.54e+01 bond pdb=" C4 ATP K 302 " pdb=" C5 ATP K 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C4 ATP V 302 " pdb=" C5 ATP V 302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP N 302 " pdb=" C5 ATP N 302 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 ... (remaining 30696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 41265 4.19 - 8.39: 260 8.39 - 12.58: 11 12.58 - 16.77: 0 16.77 - 20.97: 22 Bond angle restraints: 41558 Sorted by residual: angle pdb=" PB ATP V 302 " pdb=" O3B ATP V 302 " pdb=" PG ATP V 302 " ideal model delta sigma weight residual 139.87 118.90 20.97 1.00e+00 1.00e+00 4.40e+02 angle pdb=" PB ATP D 302 " pdb=" O3B ATP D 302 " pdb=" PG ATP D 302 " ideal model delta sigma weight residual 139.87 118.91 20.96 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP R 302 " pdb=" O3B ATP R 302 " pdb=" PG ATP R 302 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP N 302 " pdb=" O3B ATP N 302 " pdb=" PG ATP N 302 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP K 302 " pdb=" O3B ATP K 302 " pdb=" PG ATP K 302 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 ... (remaining 41553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 16760 17.27 - 34.54: 1704 34.54 - 51.80: 341 51.80 - 69.07: 115 69.07 - 86.34: 44 Dihedral angle restraints: 18964 sinusoidal: 7711 harmonic: 11253 Sorted by residual: dihedral pdb=" CA MET G 132 " pdb=" C MET G 132 " pdb=" N TYR G 133 " pdb=" CA TYR G 133 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET C 132 " pdb=" C MET C 132 " pdb=" N TYR C 133 " pdb=" CA TYR C 133 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA MET U 132 " pdb=" C MET U 132 " pdb=" N TYR U 133 " pdb=" CA TYR U 133 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 18961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2462 0.031 - 0.063: 1485 0.063 - 0.094: 538 0.094 - 0.126: 299 0.126 - 0.157: 133 Chirality restraints: 4917 Sorted by residual: chirality pdb=" CA ILE P 195 " pdb=" N ILE P 195 " pdb=" C ILE P 195 " pdb=" CB ILE P 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ILE L 195 " pdb=" N ILE L 195 " pdb=" C ILE L 195 " pdb=" CB ILE L 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE T 195 " pdb=" N ILE T 195 " pdb=" C ILE T 195 " pdb=" CB ILE T 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 4914 not shown) Planarity restraints: 5313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 224 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO M 225 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO M 225 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 225 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 224 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO C 225 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL U 224 " 0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO U 225 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO U 225 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO U 225 " 0.022 5.00e-02 4.00e+02 ... (remaining 5310 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 251 2.58 - 3.16: 23444 3.16 - 3.74: 45582 3.74 - 4.32: 69624 4.32 - 4.90: 115924 Nonbonded interactions: 254825 Sorted by model distance: nonbonded pdb=" OG1 THR J 17 " pdb="MG MG J 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR U 17 " pdb="MG MG U 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR M 17 " pdb="MG MG M 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR Q 17 " pdb="MG MG Q 301 " model vdw 2.001 2.170 nonbonded pdb=" OG1 THR C 17 " pdb="MG MG C 301 " model vdw 2.001 2.170 ... (remaining 254820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.470 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.006 0.081 30712 Z= 0.361 Angle : 1.004 20.967 41558 Z= 0.684 Chirality : 0.052 0.157 4917 Planarity : 0.004 0.039 5313 Dihedral : 15.466 86.339 11748 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.10), residues: 3927 helix: -4.03 (0.07), residues: 1320 sheet: -2.32 (0.15), residues: 935 loop : -1.99 (0.13), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 181 TYR 0.016 0.002 TYR R 182 PHE 0.021 0.003 PHE D 60 TRP 0.016 0.003 TRP T 245 HIS 0.006 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00588 (30701) covalent geometry : angle 1.00356 (41558) hydrogen bonds : bond 0.26686 ( 1197) hydrogen bonds : angle 9.18644 ( 3294) Misc. bond : bond 0.01435 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 704 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 ARG cc_start: 0.8208 (tmt-80) cc_final: 0.7979 (tpt90) REVERT: C 189 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7413 (mttm) REVERT: D 162 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7562 (mmtp) REVERT: D 168 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7088 (mttp) REVERT: E 241 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6829 (mtm-85) REVERT: G 93 ASP cc_start: 0.6104 (p0) cc_final: 0.5451 (t0) REVERT: G 94 LYS cc_start: 0.5047 (mtmm) cc_final: 0.4687 (pttt) REVERT: G 112 ASP cc_start: 0.7034 (m-30) cc_final: 0.6773 (m-30) REVERT: G 192 MET cc_start: 0.7280 (mtp) cc_final: 0.7006 (mtp) REVERT: G 253 ARG cc_start: 0.4927 (mtm180) cc_final: 0.3691 (mtt-85) REVERT: H 192 ASP cc_start: 0.7455 (p0) cc_final: 0.6994 (t0) REVERT: H 241 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6876 (ttm110) REVERT: J 77 ASP cc_start: 0.7640 (m-30) cc_final: 0.7264 (t0) REVERT: J 193 LEU cc_start: 0.7922 (mt) cc_final: 0.7680 (mp) REVERT: J 197 ASP cc_start: 0.7477 (m-30) cc_final: 0.7178 (m-30) REVERT: J 231 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7964 (mm110) REVERT: K 65 ASN cc_start: 0.7608 (m-40) cc_final: 0.7341 (m110) REVERT: K 162 LYS cc_start: 0.7029 (mtpt) cc_final: 0.6795 (mmtt) REVERT: K 176 HIS cc_start: 0.6933 (m-70) cc_final: 0.6431 (m170) REVERT: M 50 MET cc_start: 0.8117 (mmm) cc_final: 0.7771 (tpt) REVERT: M 78 LYS cc_start: 0.7513 (pttp) cc_final: 0.6996 (mmtt) REVERT: M 95 ASP cc_start: 0.7571 (p0) cc_final: 0.6925 (t0) REVERT: N 53 GLU cc_start: 0.8315 (pt0) cc_final: 0.8009 (pt0) REVERT: N 112 ASP cc_start: 0.6655 (m-30) cc_final: 0.6414 (m-30) REVERT: N 162 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7499 (mttt) REVERT: N 168 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7434 (mtpp) REVERT: N 199 GLU cc_start: 0.8156 (tt0) cc_final: 0.7500 (tp30) REVERT: O 161 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8289 (mtpt) REVERT: O 233 TYR cc_start: 0.8930 (p90) cc_final: 0.8593 (p90) REVERT: P 204 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7784 (mtm180) REVERT: Q 3 LYS cc_start: 0.7559 (ttmm) cc_final: 0.7039 (mttp) REVERT: R 3 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7694 (tppt) REVERT: R 162 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7587 (mtmt) REVERT: T 204 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7695 (mtm180) REVERT: T 240 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7387 (mtt180) REVERT: T 262 ARG cc_start: 0.8241 (tmt-80) cc_final: 0.7970 (tpp80) REVERT: U 155 MET cc_start: 0.7871 (tpp) cc_final: 0.7664 (tpt) REVERT: U 192 MET cc_start: 0.8768 (mtp) cc_final: 0.8547 (mtm) REVERT: U 196 ASP cc_start: 0.8342 (m-30) cc_final: 0.8067 (m-30) REVERT: U 199 GLU cc_start: 0.8251 (tt0) cc_final: 0.7602 (tp30) REVERT: V 112 ASP cc_start: 0.7944 (m-30) cc_final: 0.6355 (t70) REVERT: V 192 MET cc_start: 0.8905 (mtp) cc_final: 0.8592 (mtm) REVERT: V 238 TYR cc_start: 0.7993 (m-80) cc_final: 0.7681 (m-80) outliers start: 0 outliers final: 0 residues processed: 704 average time/residue: 0.2226 time to fit residues: 232.9367 Evaluate side-chains 459 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 143 ASN D 62 ASN D 65 ASN D 176 HIS G 45 ASN G 65 ASN H 259 ASN I 259 ASN J 65 ASN K 62 ASN K 65 ASN K 176 HIS M 65 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN N 62 ASN N 176 HIS Q 65 ASN R 62 ASN R 65 ASN R 176 HIS T 250 HIS T 259 ASN U 65 ASN V 62 ASN V 65 ASN V 176 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.123023 restraints weight = 35001.212| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.83 r_work: 0.3109 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30712 Z= 0.199 Angle : 0.671 10.923 41558 Z= 0.343 Chirality : 0.047 0.181 4917 Planarity : 0.005 0.049 5313 Dihedral : 10.413 89.480 4653 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.54 % Allowed : 16.96 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.12), residues: 3927 helix: -2.29 (0.11), residues: 1375 sheet: -1.60 (0.15), residues: 1023 loop : -1.65 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 55 TYR 0.014 0.002 TYR O 198 PHE 0.020 0.002 PHE V 113 TRP 0.003 0.001 TRP B 245 HIS 0.004 0.001 HIS S 250 Details of bonding type rmsd covalent geometry : bond 0.00481 (30701) covalent geometry : angle 0.67100 (41558) hydrogen bonds : bond 0.04228 ( 1197) hydrogen bonds : angle 5.28149 ( 3294) Misc. bond : bond 0.00458 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 519 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8179 (mtp) cc_final: 0.7892 (mtt) REVERT: A 254 SER cc_start: 0.7520 (p) cc_final: 0.7255 (m) REVERT: A 261 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6952 (m) REVERT: B 202 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7575 (mtm180) REVERT: C 185 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7917 (tm-30) REVERT: C 189 LYS cc_start: 0.6995 (mtpp) cc_final: 0.6751 (mttm) REVERT: C 192 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8295 (mtt) REVERT: E 204 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7484 (mtm180) REVERT: E 262 ARG cc_start: 0.6990 (tpt90) cc_final: 0.6747 (tpt90) REVERT: F 168 MET cc_start: 0.7879 (mtt) cc_final: 0.7565 (mtt) REVERT: F 233 TYR cc_start: 0.8633 (p90) cc_final: 0.8174 (p90) REVERT: F 234 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8151 (tttt) REVERT: G 9 SER cc_start: 0.8758 (t) cc_final: 0.8318 (p) REVERT: G 45 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: G 93 ASP cc_start: 0.4889 (p0) cc_final: 0.4301 (t0) REVERT: G 155 MET cc_start: 0.6398 (mmm) cc_final: 0.6136 (mmm) REVERT: G 176 HIS cc_start: 0.5679 (m90) cc_final: 0.5112 (m170) REVERT: G 253 ARG cc_start: 0.4763 (mtm180) cc_final: 0.2884 (mtt-85) REVERT: J 77 ASP cc_start: 0.7689 (m-30) cc_final: 0.6961 (t0) REVERT: J 95 ASP cc_start: 0.7263 (p0) cc_final: 0.6501 (t70) REVERT: J 185 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6854 (tt0) REVERT: J 231 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7892 (mm110) REVERT: J 238 TYR cc_start: 0.7682 (m-80) cc_final: 0.7292 (m-80) REVERT: K 54 ARG cc_start: 0.7336 (mtt90) cc_final: 0.7082 (mmt180) REVERT: K 162 LYS cc_start: 0.6414 (mtpt) cc_final: 0.6179 (mmtt) REVERT: K 174 LYS cc_start: 0.7255 (tttt) cc_final: 0.6745 (tppt) REVERT: K 176 HIS cc_start: 0.7270 (m90) cc_final: 0.6937 (m170) REVERT: K 189 LYS cc_start: 0.6675 (mtpp) cc_final: 0.6406 (mttm) REVERT: M 78 LYS cc_start: 0.7765 (pttp) cc_final: 0.7231 (mmtt) REVERT: M 95 ASP cc_start: 0.7994 (p0) cc_final: 0.7359 (t70) REVERT: N 53 GLU cc_start: 0.7818 (pt0) cc_final: 0.7583 (pt0) REVERT: N 196 ASP cc_start: 0.8104 (m-30) cc_final: 0.7870 (m-30) REVERT: N 199 GLU cc_start: 0.7746 (tt0) cc_final: 0.7434 (tp30) REVERT: O 161 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8071 (mtpt) REVERT: O 168 MET cc_start: 0.7936 (mtp) cc_final: 0.7711 (mtt) REVERT: P 204 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7441 (mtm180) REVERT: P 262 ARG cc_start: 0.6847 (tpt90) cc_final: 0.6619 (tpt90) REVERT: Q 3 LYS cc_start: 0.7389 (ttmm) cc_final: 0.7093 (mtmt) REVERT: Q 53 GLU cc_start: 0.7678 (pt0) cc_final: 0.7374 (pt0) REVERT: Q 58 TYR cc_start: 0.8194 (m-80) cc_final: 0.7689 (m-80) REVERT: Q 162 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7200 (mtpt) REVERT: Q 199 GLU cc_start: 0.8095 (tt0) cc_final: 0.7857 (tt0) REVERT: R 95 ASP cc_start: 0.7893 (p0) cc_final: 0.7647 (p0) REVERT: R 155 MET cc_start: 0.7996 (mmm) cc_final: 0.7709 (tpt) REVERT: R 192 MET cc_start: 0.8920 (mtp) cc_final: 0.8699 (mtm) REVERT: R 197 ASP cc_start: 0.8084 (m-30) cc_final: 0.7774 (m-30) REVERT: S 240 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7278 (mtp180) REVERT: S 247 LYS cc_start: 0.7572 (mttm) cc_final: 0.7341 (mttm) REVERT: T 261 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6867 (m) REVERT: U 77 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7655 (t70) REVERT: U 199 GLU cc_start: 0.7849 (tt0) cc_final: 0.7442 (tp30) REVERT: V 54 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7382 (mtp180) REVERT: V 71 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7563 (p) REVERT: V 192 MET cc_start: 0.8916 (mtp) cc_final: 0.8640 (mtm) outliers start: 113 outliers final: 61 residues processed: 606 average time/residue: 0.2119 time to fit residues: 195.0281 Evaluate side-chains 478 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 410 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 45 ASN Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 120 SER Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 120 SER Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 250 HIS Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain T residue 261 THR Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 290 optimal weight: 4.9990 chunk 207 optimal weight: 0.0970 chunk 226 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 293 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 250 HIS D 176 HIS E 250 HIS E 259 ASN F 250 HIS F 259 ASN G 45 ASN K 176 HIS M 72 GLN N 45 ASN P 250 HIS P 259 ASN ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 HIS T 259 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.152774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124489 restraints weight = 35015.306| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.61 r_work: 0.3166 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30712 Z= 0.129 Angle : 0.547 6.332 41558 Z= 0.283 Chirality : 0.044 0.173 4917 Planarity : 0.004 0.038 5313 Dihedral : 9.565 89.673 4653 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.01 % Allowed : 19.56 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 3927 helix: -1.13 (0.14), residues: 1243 sheet: -1.31 (0.15), residues: 1023 loop : -1.36 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 92 TYR 0.020 0.001 TYR N 182 PHE 0.010 0.001 PHE Q 113 TRP 0.006 0.001 TRP I 245 HIS 0.008 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00312 (30701) covalent geometry : angle 0.54728 (41558) hydrogen bonds : bond 0.03630 ( 1197) hydrogen bonds : angle 4.61400 ( 3294) Misc. bond : bond 0.00296 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 456 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.7265 (p) cc_final: 0.6993 (m) REVERT: A 261 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.7114 (m) REVERT: B 177 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 202 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7817 (mtm-85) REVERT: C 77 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: C 176 HIS cc_start: 0.7330 (m170) cc_final: 0.7092 (m170) REVERT: C 189 LYS cc_start: 0.6942 (mtpp) cc_final: 0.6712 (mttm) REVERT: D 74 LEU cc_start: 0.8108 (mp) cc_final: 0.7741 (mp) REVERT: E 204 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7601 (mtm180) REVERT: E 262 ARG cc_start: 0.7111 (tpt90) cc_final: 0.6862 (tpt90) REVERT: F 168 MET cc_start: 0.7973 (mtt) cc_final: 0.7658 (mtt) REVERT: F 233 TYR cc_start: 0.8691 (p90) cc_final: 0.8408 (p90) REVERT: F 234 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8074 (tttt) REVERT: G 9 SER cc_start: 0.8803 (t) cc_final: 0.8364 (p) REVERT: G 93 ASP cc_start: 0.4802 (p0) cc_final: 0.4258 (t0) REVERT: G 155 MET cc_start: 0.6583 (mmm) cc_final: 0.6342 (mmm) REVERT: G 176 HIS cc_start: 0.5773 (m90) cc_final: 0.5468 (m-70) REVERT: G 192 MET cc_start: 0.7783 (mtp) cc_final: 0.7218 (mtp) REVERT: J 77 ASP cc_start: 0.7711 (m-30) cc_final: 0.6905 (t0) REVERT: J 95 ASP cc_start: 0.7431 (p0) cc_final: 0.6517 (t70) REVERT: J 112 ASP cc_start: 0.7339 (m-30) cc_final: 0.6999 (t0) REVERT: J 231 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7950 (mm110) REVERT: J 238 TYR cc_start: 0.7720 (m-80) cc_final: 0.7306 (m-80) REVERT: K 54 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7124 (mmm-85) REVERT: K 174 LYS cc_start: 0.7039 (tttt) cc_final: 0.6526 (tppt) REVERT: K 176 HIS cc_start: 0.7196 (m-70) cc_final: 0.6374 (m170) REVERT: K 189 LYS cc_start: 0.6580 (mtpp) cc_final: 0.6331 (mttm) REVERT: L 177 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8426 (tp) REVERT: M 54 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7291 (mtp180) REVERT: M 78 LYS cc_start: 0.7705 (pttp) cc_final: 0.7252 (mmtt) REVERT: M 238 TYR cc_start: 0.7818 (m-80) cc_final: 0.7610 (m-80) REVERT: M 240 ASP cc_start: 0.7553 (m-30) cc_final: 0.7350 (m-30) REVERT: N 53 GLU cc_start: 0.7888 (pt0) cc_final: 0.7673 (pt0) REVERT: N 77 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7333 (t0) REVERT: N 196 ASP cc_start: 0.8179 (m-30) cc_final: 0.7775 (m-30) REVERT: N 199 GLU cc_start: 0.7956 (tt0) cc_final: 0.7401 (tp30) REVERT: O 158 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7454 (ttpt) REVERT: O 161 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8082 (mtpt) REVERT: O 168 MET cc_start: 0.8050 (mtp) cc_final: 0.7579 (mtt) REVERT: P 204 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7412 (mtm180) REVERT: P 262 ARG cc_start: 0.7022 (tpt90) cc_final: 0.6786 (tpt90) REVERT: Q 3 LYS cc_start: 0.7485 (ttmm) cc_final: 0.7254 (tppt) REVERT: Q 53 GLU cc_start: 0.7702 (pt0) cc_final: 0.7410 (pt0) REVERT: R 155 MET cc_start: 0.8005 (mmm) cc_final: 0.7693 (tpt) REVERT: U 77 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7607 (t70) REVERT: U 199 GLU cc_start: 0.7961 (tt0) cc_final: 0.7640 (tp30) REVERT: V 54 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7434 (mtp180) REVERT: V 112 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6405 (t0) outliers start: 96 outliers final: 65 residues processed: 524 average time/residue: 0.2016 time to fit residues: 162.9571 Evaluate side-chains 477 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 404 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 263 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 363 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 72 GLN C 176 HIS E 259 ASN G 45 ASN ** H 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 HIS ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 HIS N 45 ASN P 259 ASN ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 HIS R 176 HIS T 259 ASN ** U 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.151716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121455 restraints weight = 34648.300| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.70 r_work: 0.3094 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 30712 Z= 0.258 Angle : 0.692 8.820 41558 Z= 0.350 Chirality : 0.049 0.174 4917 Planarity : 0.004 0.039 5313 Dihedral : 9.627 79.047 4653 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.64 % Allowed : 20.31 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.12), residues: 3927 helix: -1.14 (0.14), residues: 1243 sheet: -1.45 (0.15), residues: 1023 loop : -1.35 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 54 TYR 0.022 0.002 TYR N 182 PHE 0.014 0.002 PHE V 113 TRP 0.006 0.001 TRP H 245 HIS 0.011 0.002 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00633 (30701) covalent geometry : angle 0.69180 (41558) hydrogen bonds : bond 0.04300 ( 1197) hydrogen bonds : angle 4.78204 ( 3294) Misc. bond : bond 0.00458 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 410 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.7451 (p) cc_final: 0.7221 (m) REVERT: A 261 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7190 (m) REVERT: B 177 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8235 (tp) REVERT: B 202 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7953 (mtm-85) REVERT: C 77 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: C 155 MET cc_start: 0.7640 (tpt) cc_final: 0.7148 (tpt) REVERT: C 176 HIS cc_start: 0.7372 (m-70) cc_final: 0.7151 (m170) REVERT: C 189 LYS cc_start: 0.7106 (mtpp) cc_final: 0.6873 (mttt) REVERT: C 199 GLU cc_start: 0.7722 (tt0) cc_final: 0.7373 (tm-30) REVERT: D 74 LEU cc_start: 0.8201 (mp) cc_final: 0.7856 (mp) REVERT: D 171 GLU cc_start: 0.6914 (tt0) cc_final: 0.6684 (tp30) REVERT: D 206 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (mp) REVERT: E 204 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7797 (mtm180) REVERT: F 177 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8332 (tp) REVERT: F 234 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8185 (tttt) REVERT: G 3 LYS cc_start: 0.5918 (ttmm) cc_final: 0.5606 (mttt) REVERT: G 93 ASP cc_start: 0.4925 (p0) cc_final: 0.4407 (t0) REVERT: G 155 MET cc_start: 0.6642 (mmm) cc_final: 0.6375 (mmm) REVERT: G 176 HIS cc_start: 0.6048 (m90) cc_final: 0.5628 (m170) REVERT: G 218 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6816 (mmtp) REVERT: H 177 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8468 (tp) REVERT: H 210 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7382 (mttp) REVERT: I 180 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7508 (mt) REVERT: J 77 ASP cc_start: 0.7928 (m-30) cc_final: 0.7063 (t0) REVERT: J 155 MET cc_start: 0.7837 (mmm) cc_final: 0.7607 (mmm) REVERT: J 231 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8034 (mm110) REVERT: J 238 TYR cc_start: 0.7891 (m-80) cc_final: 0.7456 (m-80) REVERT: K 174 LYS cc_start: 0.7167 (tttt) cc_final: 0.6707 (tppt) REVERT: K 192 MET cc_start: 0.8800 (mtt) cc_final: 0.8389 (mtp) REVERT: K 244 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6737 (mtt180) REVERT: L 177 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8507 (tp) REVERT: L 210 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7545 (mttp) REVERT: L 234 LYS cc_start: 0.8774 (tptm) cc_final: 0.8566 (tttt) REVERT: M 54 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7567 (mtp180) REVERT: M 78 LYS cc_start: 0.7860 (pttp) cc_final: 0.7404 (mmtt) REVERT: M 155 MET cc_start: 0.8025 (tpp) cc_final: 0.7779 (tpt) REVERT: M 240 ASP cc_start: 0.7604 (m-30) cc_final: 0.7389 (m-30) REVERT: N 77 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7558 (t0) REVERT: N 199 GLU cc_start: 0.8048 (tt0) cc_final: 0.7588 (tp30) REVERT: O 158 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7559 (ttpt) REVERT: O 161 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8110 (mtpt) REVERT: O 168 MET cc_start: 0.8078 (mtp) cc_final: 0.7689 (mtt) REVERT: O 177 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8236 (tp) REVERT: P 204 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7584 (mtm180) REVERT: Q 3 LYS cc_start: 0.7586 (ttmm) cc_final: 0.7360 (tppt) REVERT: Q 53 GLU cc_start: 0.7929 (pt0) cc_final: 0.7634 (pt0) REVERT: R 155 MET cc_start: 0.8244 (mmm) cc_final: 0.7973 (tpt) REVERT: S 177 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8275 (tp) REVERT: U 77 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7762 (t70) REVERT: U 199 GLU cc_start: 0.8119 (tt0) cc_final: 0.7832 (tp30) REVERT: V 54 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7533 (mtp180) outliers start: 148 outliers final: 96 residues processed: 523 average time/residue: 0.2015 time to fit residues: 162.3920 Evaluate side-chains 500 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 390 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 250 HIS Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 45 ASN Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 244 ARG Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 148 SER Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 286 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 187 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 72 GLN E 259 ASN K 72 GLN N 45 ASN P 259 ASN Q 72 GLN Q 176 HIS T 259 ASN ** U 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.154942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124578 restraints weight = 34483.669| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.94 r_work: 0.3084 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30712 Z= 0.121 Angle : 0.528 6.544 41558 Z= 0.273 Chirality : 0.044 0.169 4917 Planarity : 0.003 0.045 5313 Dihedral : 9.233 81.384 4653 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.61 % Allowed : 22.01 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3927 helix: -0.61 (0.14), residues: 1243 sheet: -1.22 (0.15), residues: 1023 loop : -1.21 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 44 TYR 0.018 0.001 TYR O 233 PHE 0.010 0.001 PHE Q 113 TRP 0.005 0.000 TRP I 245 HIS 0.010 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00293 (30701) covalent geometry : angle 0.52827 (41558) hydrogen bonds : bond 0.03222 ( 1197) hydrogen bonds : angle 4.33574 ( 3294) Misc. bond : bond 0.00301 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 422 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.7479 (p) cc_final: 0.7238 (m) REVERT: A 261 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7209 (m) REVERT: B 177 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (tp) REVERT: B 202 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7915 (mtm-85) REVERT: C 77 ASP cc_start: 0.7992 (m-30) cc_final: 0.7747 (m-30) REVERT: C 155 MET cc_start: 0.7639 (tpt) cc_final: 0.6996 (tpt) REVERT: D 74 LEU cc_start: 0.8112 (mp) cc_final: 0.7898 (mp) REVERT: E 204 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7713 (mtm180) REVERT: F 234 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8120 (tttt) REVERT: G 3 LYS cc_start: 0.6080 (ttmm) cc_final: 0.5781 (mttt) REVERT: G 93 ASP cc_start: 0.4890 (p0) cc_final: 0.4493 (t0) REVERT: G 155 MET cc_start: 0.6577 (mmm) cc_final: 0.6338 (mmm) REVERT: G 176 HIS cc_start: 0.6140 (m90) cc_final: 0.5767 (m90) REVERT: G 192 MET cc_start: 0.7677 (mtp) cc_final: 0.7042 (mtp) REVERT: H 177 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8478 (tp) REVERT: H 250 HIS cc_start: 0.7567 (t-170) cc_final: 0.7175 (t-170) REVERT: I 180 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7395 (mt) REVERT: J 77 ASP cc_start: 0.7794 (m-30) cc_final: 0.6976 (t0) REVERT: K 174 LYS cc_start: 0.7085 (tttt) cc_final: 0.6634 (tppt) REVERT: L 177 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8440 (tp) REVERT: M 54 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7474 (mtp180) REVERT: M 78 LYS cc_start: 0.7857 (pttp) cc_final: 0.7414 (mmtt) REVERT: M 192 MET cc_start: 0.8869 (mtp) cc_final: 0.8663 (mtp) REVERT: M 238 TYR cc_start: 0.7826 (m-80) cc_final: 0.7572 (m-80) REVERT: M 240 ASP cc_start: 0.7341 (m-30) cc_final: 0.7111 (m-30) REVERT: N 77 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7388 (t0) REVERT: O 158 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7543 (ttpt) REVERT: O 161 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8062 (mtpt) REVERT: O 168 MET cc_start: 0.8082 (mtp) cc_final: 0.7639 (mtt) REVERT: P 204 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7492 (mtm180) REVERT: Q 53 GLU cc_start: 0.7613 (pt0) cc_final: 0.7349 (pt0) REVERT: Q 155 MET cc_start: 0.7988 (tpt) cc_final: 0.7773 (mmm) REVERT: R 155 MET cc_start: 0.8009 (mmm) cc_final: 0.7705 (tpt) REVERT: S 177 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8240 (tp) REVERT: U 77 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7618 (t70) REVERT: U 199 GLU cc_start: 0.7857 (tt0) cc_final: 0.7548 (tp30) REVERT: V 54 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7510 (mtp180) outliers start: 115 outliers final: 84 residues processed: 504 average time/residue: 0.2085 time to fit residues: 160.6026 Evaluate side-chains 490 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 397 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 205 optimal weight: 0.9980 chunk 342 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN E 259 ASN L 259 ASN O 259 ASN P 259 ASN Q 72 GLN Q 176 HIS R 176 HIS T 259 ASN ** U 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118783 restraints weight = 34596.620| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.90 r_work: 0.3091 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 30712 Z= 0.239 Angle : 0.667 8.602 41558 Z= 0.336 Chirality : 0.048 0.175 4917 Planarity : 0.004 0.046 5313 Dihedral : 9.498 87.358 4653 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.61 % Allowed : 21.94 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3927 helix: -0.80 (0.14), residues: 1243 sheet: -1.27 (0.15), residues: 1001 loop : -1.21 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 54 TYR 0.021 0.002 TYR N 182 PHE 0.016 0.002 PHE R 113 TRP 0.004 0.001 TRP I 245 HIS 0.010 0.001 HIS F 250 Details of bonding type rmsd covalent geometry : bond 0.00586 (30701) covalent geometry : angle 0.66722 (41558) hydrogen bonds : bond 0.04016 ( 1197) hydrogen bonds : angle 4.58850 ( 3294) Misc. bond : bond 0.00428 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 401 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 SER cc_start: 0.7419 (p) cc_final: 0.7177 (m) REVERT: A 261 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7265 (m) REVERT: B 177 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8277 (tp) REVERT: B 202 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7958 (mtm-85) REVERT: C 77 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: C 155 MET cc_start: 0.7643 (tpt) cc_final: 0.7057 (tpt) REVERT: C 167 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7069 (pt0) REVERT: C 185 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 199 GLU cc_start: 0.7787 (tt0) cc_final: 0.7484 (tm-30) REVERT: D 74 LEU cc_start: 0.8121 (mp) cc_final: 0.7846 (mp) REVERT: D 206 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7993 (mp) REVERT: E 204 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7821 (mtm180) REVERT: E 250 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: F 189 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7426 (mt) REVERT: F 234 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (tttt) REVERT: G 3 LYS cc_start: 0.6048 (ttmm) cc_final: 0.5672 (mttt) REVERT: G 93 ASP cc_start: 0.4772 (p0) cc_final: 0.4410 (t0) REVERT: G 155 MET cc_start: 0.6652 (mmm) cc_final: 0.6394 (mmm) REVERT: G 176 HIS cc_start: 0.6028 (m90) cc_final: 0.5557 (m170) REVERT: G 192 MET cc_start: 0.7606 (mtp) cc_final: 0.6962 (mtp) REVERT: H 177 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8527 (tp) REVERT: H 210 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7595 (mttp) REVERT: H 250 HIS cc_start: 0.7757 (t-170) cc_final: 0.7398 (t-170) REVERT: I 180 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7284 (mt) REVERT: J 77 ASP cc_start: 0.7887 (m-30) cc_final: 0.6992 (t0) REVERT: K 174 LYS cc_start: 0.7139 (tttt) cc_final: 0.6674 (tppt) REVERT: K 192 MET cc_start: 0.8800 (mtp) cc_final: 0.8589 (mtt) REVERT: K 199 GLU cc_start: 0.7686 (tt0) cc_final: 0.7144 (tm-30) REVERT: L 177 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8536 (tp) REVERT: M 54 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7517 (mtp180) REVERT: M 78 LYS cc_start: 0.7833 (pttp) cc_final: 0.7325 (mmtt) REVERT: M 238 TYR cc_start: 0.7916 (m-80) cc_final: 0.7560 (m-80) REVERT: M 240 ASP cc_start: 0.7565 (m-30) cc_final: 0.7342 (m-30) REVERT: N 77 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7614 (t0) REVERT: O 158 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7423 (ttpp) REVERT: O 161 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8059 (mtpt) REVERT: O 168 MET cc_start: 0.8017 (mtp) cc_final: 0.7563 (mtt) REVERT: O 177 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8283 (tp) REVERT: P 204 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7587 (mtm180) REVERT: Q 53 GLU cc_start: 0.7870 (pt0) cc_final: 0.7624 (pt0) REVERT: R 155 MET cc_start: 0.8251 (mmm) cc_final: 0.7958 (tpt) REVERT: S 177 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8268 (tp) REVERT: U 77 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7797 (t70) REVERT: U 117 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8033 (mm) REVERT: U 199 GLU cc_start: 0.8128 (tt0) cc_final: 0.7856 (tp30) REVERT: V 54 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7525 (mtp180) outliers start: 147 outliers final: 102 residues processed: 514 average time/residue: 0.2106 time to fit residues: 164.7403 Evaluate side-chains 496 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 379 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 250 HIS Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 181 ARG Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 250 HIS Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 81 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 185 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 176 HIS E 259 ASN K 176 HIS P 259 ASN Q 72 GLN Q 176 HIS R 176 HIS R 222 GLN T 259 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.155395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127307 restraints weight = 34405.396| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.54 r_work: 0.3207 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 30712 Z= 0.143 Angle : 0.558 7.200 41558 Z= 0.286 Chirality : 0.044 0.169 4917 Planarity : 0.004 0.047 5313 Dihedral : 9.266 89.486 4653 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.23 % Allowed : 22.70 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 3927 helix: -0.45 (0.14), residues: 1243 sheet: -1.25 (0.15), residues: 1023 loop : -1.17 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.018 0.002 TYR N 182 PHE 0.012 0.001 PHE R 113 TRP 0.005 0.001 TRP I 245 HIS 0.009 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00351 (30701) covalent geometry : angle 0.55815 (41558) hydrogen bonds : bond 0.03331 ( 1197) hydrogen bonds : angle 4.31590 ( 3294) Misc. bond : bond 0.00329 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 408 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7308 (m) REVERT: B 177 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8275 (tp) REVERT: B 202 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7964 (mtm-85) REVERT: C 77 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: C 155 MET cc_start: 0.7677 (tpt) cc_final: 0.7070 (tpt) REVERT: C 167 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7057 (pt0) REVERT: C 185 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7964 (tm-30) REVERT: D 74 LEU cc_start: 0.8249 (mp) cc_final: 0.8032 (mp) REVERT: D 206 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7928 (mp) REVERT: E 204 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7769 (mtm180) REVERT: F 189 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7337 (mt) REVERT: F 234 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8147 (tttt) REVERT: G 3 LYS cc_start: 0.6105 (ttmm) cc_final: 0.5734 (mttt) REVERT: G 93 ASP cc_start: 0.4871 (p0) cc_final: 0.4508 (t0) REVERT: G 155 MET cc_start: 0.6633 (mmm) cc_final: 0.6387 (mmm) REVERT: G 176 HIS cc_start: 0.6112 (m90) cc_final: 0.5645 (m170) REVERT: G 192 MET cc_start: 0.7665 (mtp) cc_final: 0.7180 (mtp) REVERT: H 177 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8501 (tp) REVERT: H 210 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7414 (mttp) REVERT: H 250 HIS cc_start: 0.7453 (t-170) cc_final: 0.7093 (t-170) REVERT: I 180 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7345 (mt) REVERT: J 77 ASP cc_start: 0.7761 (m-30) cc_final: 0.6928 (t0) REVERT: K 174 LYS cc_start: 0.7131 (tttt) cc_final: 0.6694 (tppt) REVERT: K 199 GLU cc_start: 0.7588 (tt0) cc_final: 0.7165 (tm-30) REVERT: L 177 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8452 (tp) REVERT: L 216 ARG cc_start: 0.8266 (mtt90) cc_final: 0.7937 (ttm110) REVERT: M 54 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7557 (mtp180) REVERT: M 78 LYS cc_start: 0.7860 (pttp) cc_final: 0.7398 (mmtt) REVERT: M 238 TYR cc_start: 0.7802 (m-80) cc_final: 0.7507 (m-80) REVERT: M 240 ASP cc_start: 0.7459 (m-30) cc_final: 0.7217 (m-30) REVERT: N 77 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7533 (t0) REVERT: O 158 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7529 (ttpp) REVERT: O 161 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8047 (mtpt) REVERT: O 168 MET cc_start: 0.8032 (mtp) cc_final: 0.7582 (mtt) REVERT: P 204 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7567 (mtm180) REVERT: Q 53 GLU cc_start: 0.7679 (pt0) cc_final: 0.7447 (pt0) REVERT: Q 155 MET cc_start: 0.8040 (tpt) cc_final: 0.7821 (mmm) REVERT: R 155 MET cc_start: 0.8098 (mmm) cc_final: 0.7826 (tpt) REVERT: S 177 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8238 (tp) REVERT: U 77 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7678 (t70) REVERT: U 199 GLU cc_start: 0.7988 (tt0) cc_final: 0.7779 (tp30) REVERT: V 54 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7518 (mtp180) outliers start: 135 outliers final: 105 residues processed: 507 average time/residue: 0.2072 time to fit residues: 160.1441 Evaluate side-chains 501 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 384 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 177 LEU Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 181 ARG Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 181 ARG Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 297 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 0.0870 chunk 249 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 344 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 176 HIS E 259 ASN G 84 HIS K 176 HIS P 259 ASN Q 72 GLN Q 176 HIS R 176 HIS T 259 ASN U 72 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.154043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.124733 restraints weight = 34355.375| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.62 r_work: 0.3190 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30712 Z= 0.148 Angle : 0.561 7.417 41558 Z= 0.286 Chirality : 0.045 0.166 4917 Planarity : 0.004 0.049 5313 Dihedral : 9.205 87.050 4653 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.23 % Allowed : 22.73 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3927 helix: -0.30 (0.15), residues: 1243 sheet: -1.21 (0.15), residues: 1023 loop : -1.13 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.019 0.002 TYR N 182 PHE 0.012 0.001 PHE R 113 TRP 0.005 0.001 TRP I 245 HIS 0.011 0.001 HIS O 250 Details of bonding type rmsd covalent geometry : bond 0.00363 (30701) covalent geometry : angle 0.56149 (41558) hydrogen bonds : bond 0.03303 ( 1197) hydrogen bonds : angle 4.25428 ( 3294) Misc. bond : bond 0.00323 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 380 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7304 (m) REVERT: B 177 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8254 (tp) REVERT: C 77 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: C 93 ASP cc_start: 0.6226 (p0) cc_final: 0.5897 (p0) REVERT: C 155 MET cc_start: 0.7673 (tpt) cc_final: 0.7055 (tpt) REVERT: C 167 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7065 (pt0) REVERT: C 185 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 74 LEU cc_start: 0.8243 (mp) cc_final: 0.8010 (mp) REVERT: D 206 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7988 (mp) REVERT: E 204 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7820 (mtm180) REVERT: F 189 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7334 (mt) REVERT: F 234 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8185 (tttt) REVERT: G 3 LYS cc_start: 0.6170 (ttmm) cc_final: 0.5842 (mttt) REVERT: G 93 ASP cc_start: 0.4839 (p0) cc_final: 0.4489 (t0) REVERT: G 155 MET cc_start: 0.6631 (mmm) cc_final: 0.6401 (mmm) REVERT: G 176 HIS cc_start: 0.6094 (m90) cc_final: 0.5633 (m170) REVERT: G 192 MET cc_start: 0.7638 (mtp) cc_final: 0.7088 (mtp) REVERT: H 177 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8542 (tp) REVERT: H 210 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7396 (mttp) REVERT: H 216 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7654 (mtt90) REVERT: I 180 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7437 (mt) REVERT: J 77 ASP cc_start: 0.7839 (m-30) cc_final: 0.7011 (t0) REVERT: K 174 LYS cc_start: 0.7160 (tttt) cc_final: 0.6741 (tppt) REVERT: K 199 GLU cc_start: 0.7623 (tt0) cc_final: 0.7143 (tm-30) REVERT: L 177 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8494 (tp) REVERT: L 216 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7956 (ttm110) REVERT: M 54 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7622 (mtp180) REVERT: M 78 LYS cc_start: 0.7814 (pttp) cc_final: 0.7360 (mmtt) REVERT: M 238 TYR cc_start: 0.7866 (m-80) cc_final: 0.7563 (m-80) REVERT: N 77 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7593 (t0) REVERT: O 158 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7529 (ttpp) REVERT: O 161 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8038 (mtpt) REVERT: O 168 MET cc_start: 0.8043 (mtp) cc_final: 0.7539 (mtt) REVERT: P 204 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7571 (mtm180) REVERT: Q 53 GLU cc_start: 0.7744 (pt0) cc_final: 0.7536 (pt0) REVERT: Q 155 MET cc_start: 0.8039 (tpt) cc_final: 0.7839 (mmm) REVERT: S 177 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8249 (tp) REVERT: U 77 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7669 (t0) REVERT: U 199 GLU cc_start: 0.8063 (tt0) cc_final: 0.7752 (tp30) REVERT: U 200 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: V 54 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7511 (mtp180) REVERT: V 112 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.6633 (t0) REVERT: V 192 MET cc_start: 0.8884 (mtp) cc_final: 0.8655 (mtm) outliers start: 135 outliers final: 111 residues processed: 483 average time/residue: 0.2090 time to fit residues: 153.5652 Evaluate side-chains 497 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 372 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 206 LEU Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 72 GLN Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 181 ARG Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 181 ARG Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 181 ARG Chi-restraints excluded: chain U residue 200 GLU Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 18 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 176 HIS E 259 ASN K 176 HIS P 259 ASN Q 72 GLN Q 176 HIS R 176 HIS T 259 ASN U 72 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.153188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.122200 restraints weight = 34559.660| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.88 r_work: 0.3131 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30712 Z= 0.180 Angle : 0.597 7.361 41558 Z= 0.303 Chirality : 0.046 0.166 4917 Planarity : 0.004 0.050 5313 Dihedral : 9.272 85.105 4653 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.58 % Allowed : 22.45 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.13), residues: 3927 helix: -0.34 (0.14), residues: 1243 sheet: -1.14 (0.15), residues: 1001 loop : -1.11 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.019 0.002 TYR A 233 PHE 0.014 0.001 PHE R 113 TRP 0.005 0.001 TRP I 245 HIS 0.010 0.001 HIS O 250 Details of bonding type rmsd covalent geometry : bond 0.00443 (30701) covalent geometry : angle 0.59679 (41558) hydrogen bonds : bond 0.03528 ( 1197) hydrogen bonds : angle 4.33743 ( 3294) Misc. bond : bond 0.00369 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 374 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7577 (OUTLIER) cc_final: 0.7293 (m) REVERT: B 177 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8273 (tp) REVERT: C 77 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: C 155 MET cc_start: 0.7571 (tpt) cc_final: 0.6962 (tpt) REVERT: C 167 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7144 (pt0) REVERT: C 185 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 74 LEU cc_start: 0.8158 (mp) cc_final: 0.7896 (mp) REVERT: D 206 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7895 (mp) REVERT: E 204 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7727 (mtm180) REVERT: F 189 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7288 (mt) REVERT: F 234 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (tttt) REVERT: G 3 LYS cc_start: 0.6141 (ttmm) cc_final: 0.5727 (mttt) REVERT: G 93 ASP cc_start: 0.4698 (p0) cc_final: 0.4382 (t0) REVERT: G 155 MET cc_start: 0.6639 (mmm) cc_final: 0.6389 (mmm) REVERT: G 176 HIS cc_start: 0.5956 (m90) cc_final: 0.5473 (m170) REVERT: G 192 MET cc_start: 0.7531 (mtp) cc_final: 0.6971 (mtp) REVERT: G 233 ASP cc_start: 0.6449 (p0) cc_final: 0.5924 (p0) REVERT: H 177 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8487 (tp) REVERT: H 210 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7385 (mttp) REVERT: H 216 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7544 (mtt90) REVERT: H 250 HIS cc_start: 0.7579 (t-170) cc_final: 0.7106 (t-170) REVERT: I 180 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7177 (mt) REVERT: J 171 GLU cc_start: 0.6977 (tt0) cc_final: 0.6736 (tp30) REVERT: K 174 LYS cc_start: 0.6989 (tttt) cc_final: 0.6545 (tppt) REVERT: L 177 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8493 (tp) REVERT: L 216 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7841 (ttm110) REVERT: M 54 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7549 (mtp180) REVERT: M 78 LYS cc_start: 0.7726 (pttp) cc_final: 0.7232 (mmtt) REVERT: M 155 MET cc_start: 0.7831 (tpp) cc_final: 0.7483 (mmt) REVERT: M 238 TYR cc_start: 0.7859 (m-80) cc_final: 0.7506 (m-80) REVERT: M 240 ASP cc_start: 0.7484 (m-30) cc_final: 0.7228 (m-30) REVERT: N 77 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7605 (t0) REVERT: O 158 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7390 (ttpp) REVERT: O 161 LYS cc_start: 0.8498 (mtmm) cc_final: 0.7996 (mtpt) REVERT: O 168 MET cc_start: 0.7899 (mtp) cc_final: 0.7363 (mtt) REVERT: P 204 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7482 (mtm180) REVERT: Q 53 GLU cc_start: 0.7796 (pt0) cc_final: 0.7550 (pt0) REVERT: R 155 MET cc_start: 0.8095 (tpt) cc_final: 0.7736 (tpt) REVERT: S 177 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8288 (tp) REVERT: U 77 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7679 (t0) REVERT: U 200 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: V 54 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7380 (mtp180) outliers start: 146 outliers final: 121 residues processed: 486 average time/residue: 0.2056 time to fit residues: 151.6254 Evaluate side-chains 508 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 374 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 206 LEU Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 189 LEU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 181 ARG Chi-restraints excluded: chain Q residue 191 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 181 ARG Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 124 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 181 ARG Chi-restraints excluded: chain U residue 200 GLU Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 179 LEU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 248 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 374 optimal weight: 0.6980 chunk 230 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 371 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 176 HIS E 259 ASN K 176 HIS P 259 ASN Q 72 GLN R 176 HIS T 259 ASN U 72 GLN ** U 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.155540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.126288 restraints weight = 34206.193| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.78 r_work: 0.3213 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30712 Z= 0.116 Angle : 0.529 7.133 41558 Z= 0.272 Chirality : 0.044 0.163 4917 Planarity : 0.003 0.051 5313 Dihedral : 9.077 83.357 4653 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.95 % Allowed : 23.20 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3927 helix: 0.01 (0.15), residues: 1243 sheet: -1.09 (0.15), residues: 1023 loop : -1.08 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.018 0.001 TYR H 233 PHE 0.009 0.001 PHE Q 113 TRP 0.005 0.000 TRP I 245 HIS 0.009 0.001 HIS O 250 Details of bonding type rmsd covalent geometry : bond 0.00282 (30701) covalent geometry : angle 0.52922 (41558) hydrogen bonds : bond 0.03041 ( 1197) hydrogen bonds : angle 4.15953 ( 3294) Misc. bond : bond 0.00277 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7854 Ramachandran restraints generated. 3927 Oldfield, 0 Emsley, 3927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 393 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7083 (m) REVERT: B 177 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8215 (tp) REVERT: C 155 MET cc_start: 0.7658 (tpt) cc_final: 0.7021 (tpt) REVERT: C 167 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7175 (pt0) REVERT: C 185 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7787 (tm-30) REVERT: D 74 LEU cc_start: 0.8230 (mp) cc_final: 0.7993 (mp) REVERT: D 206 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7858 (mp) REVERT: E 204 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7743 (mtm180) REVERT: F 189 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7248 (mt) REVERT: F 234 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8099 (tttt) REVERT: G 3 LYS cc_start: 0.6165 (ttmm) cc_final: 0.5752 (mttt) REVERT: G 93 ASP cc_start: 0.4869 (p0) cc_final: 0.4608 (t0) REVERT: G 106 MET cc_start: 0.6969 (mmm) cc_final: 0.6755 (mmm) REVERT: G 155 MET cc_start: 0.6604 (mmm) cc_final: 0.6375 (mmm) REVERT: G 176 HIS cc_start: 0.6098 (m90) cc_final: 0.5626 (m170) REVERT: G 192 MET cc_start: 0.7575 (mtp) cc_final: 0.7065 (mtp) REVERT: G 233 ASP cc_start: 0.6459 (p0) cc_final: 0.5955 (p0) REVERT: H 177 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8485 (tp) REVERT: H 210 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7339 (mttp) REVERT: H 216 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7731 (ttm110) REVERT: H 250 HIS cc_start: 0.7361 (t-170) cc_final: 0.6900 (t-170) REVERT: I 180 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7335 (mt) REVERT: K 174 LYS cc_start: 0.7141 (tttt) cc_final: 0.6801 (ttmm) REVERT: K 176 HIS cc_start: 0.7591 (m-70) cc_final: 0.7339 (m170) REVERT: K 199 GLU cc_start: 0.7399 (tt0) cc_final: 0.7197 (tm-30) REVERT: L 177 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8445 (tp) REVERT: L 216 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7970 (ttm110) REVERT: M 54 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7536 (mtp180) REVERT: M 78 LYS cc_start: 0.7849 (pttp) cc_final: 0.7509 (mmtt) REVERT: M 155 MET cc_start: 0.7652 (tpp) cc_final: 0.7313 (mmt) REVERT: M 238 TYR cc_start: 0.7771 (m-80) cc_final: 0.7498 (m-80) REVERT: M 240 ASP cc_start: 0.7194 (m-30) cc_final: 0.6975 (m-30) REVERT: N 77 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7399 (t0) REVERT: O 158 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7511 (ttpp) REVERT: O 161 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8026 (mtpt) REVERT: O 168 MET cc_start: 0.7966 (mtp) cc_final: 0.7546 (mtt) REVERT: Q 53 GLU cc_start: 0.7481 (pt0) cc_final: 0.7246 (pt0) REVERT: Q 155 MET cc_start: 0.7971 (tpt) cc_final: 0.7767 (mmm) REVERT: Q 175 GLU cc_start: 0.7180 (pt0) cc_final: 0.6976 (mt-10) REVERT: R 155 MET cc_start: 0.7980 (tpt) cc_final: 0.7676 (tpt) REVERT: S 177 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8222 (tp) REVERT: U 77 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7022 (t0) REVERT: U 117 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7962 (mm) REVERT: U 200 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: V 54 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7357 (mtp180) REVERT: V 112 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6685 (t0) REVERT: V 192 MET cc_start: 0.8860 (mtp) cc_final: 0.8651 (mtm) outliers start: 126 outliers final: 105 residues processed: 484 average time/residue: 0.2011 time to fit residues: 149.1691 Evaluate side-chains 497 residues out of total 3190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 378 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 200 GLU Chi-restraints excluded: chain K residue 206 LEU Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 181 ARG Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 112 ASP Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 206 LEU Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 228 SER Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 261 THR Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 261 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 132 MET Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 181 ARG Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 103 GLU Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 181 ARG Chi-restraints excluded: chain R residue 200 GLU Chi-restraints excluded: chain S residue 177 LEU Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 228 SER Chi-restraints excluded: chain S residue 249 VAL Chi-restraints excluded: chain S residue 254 SER Chi-restraints excluded: chain S residue 261 THR Chi-restraints excluded: chain T residue 190 LEU Chi-restraints excluded: chain T residue 228 SER Chi-restraints excluded: chain T residue 249 VAL Chi-restraints excluded: chain U residue 77 ASP Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 112 ASP Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain U residue 132 MET Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain U residue 181 ARG Chi-restraints excluded: chain U residue 200 GLU Chi-restraints excluded: chain U residue 242 VAL Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 112 ASP Chi-restraints excluded: chain V residue 132 MET Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain V residue 175 GLU Chi-restraints excluded: chain V residue 179 LEU Chi-restraints excluded: chain V residue 181 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 1 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 269 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN C 143 ASN C 176 HIS E 259 ASN ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 ASN P 259 ASN Q 176 HIS R 65 ASN R 176 HIS R 222 GLN T 259 ASN U 65 ASN ** U 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 222 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.150254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.120051 restraints weight = 34882.733| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.89 r_work: 0.3042 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 30712 Z= 0.326 Angle : 0.766 9.839 41558 Z= 0.384 Chirality : 0.052 0.177 4917 Planarity : 0.005 0.061 5313 Dihedral : 9.549 81.467 4653 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.33 % Allowed : 22.92 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3927 helix: -0.67 (0.14), residues: 1243 sheet: -1.27 (0.15), residues: 1001 loop : -1.19 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 181 TYR 0.021 0.002 TYR O 233 PHE 0.020 0.002 PHE R 113 TRP 0.005 0.001 TRP I 245 HIS 0.011 0.002 HIS O 250 Details of bonding type rmsd covalent geometry : bond 0.00795 (30701) covalent geometry : angle 0.76561 (41558) hydrogen bonds : bond 0.04466 ( 1197) hydrogen bonds : angle 4.76418 ( 3294) Misc. bond : bond 0.00548 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7307.94 seconds wall clock time: 126 minutes 1.71 seconds (7561.71 seconds total)