Starting phenix.real_space_refine on Sat Feb 7 13:36:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvc_38696/02_2026/8xvc_38696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvc_38696/02_2026/8xvc_38696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xvc_38696/02_2026/8xvc_38696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvc_38696/02_2026/8xvc_38696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xvc_38696/02_2026/8xvc_38696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvc_38696/02_2026/8xvc_38696.map" } resolution = 4.32 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 162 5.16 5 C 21006 2.51 5 N 6264 2.21 5 O 6372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33840 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "C" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "D" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "E" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "F" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "G" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "H" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "I" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "J" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "K" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "L" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "M" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "N" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "O" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "P" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "Q" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "R" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.45, per 1000 atoms: 0.19 Number of scatterers: 33840 At special positions: 0 Unit cell: (166.46, 164, 86.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 P 36 15.00 O 6372 8.00 N 6264 7.00 C 21006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7956 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 18 sheets defined 64.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 76 through 93 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA A 130 " --> pdb=" O PRO A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'B' and resid 76 through 93 Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU B 178 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 265 through 284 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'C' and resid 76 through 93 Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA C 130 " --> pdb=" O PRO C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU C 178 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 265 through 284 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'D' and resid 76 through 93 Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA D 130 " --> pdb=" O PRO D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.762A pdb=" N LEU D 178 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 192 Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 265 through 284 Processing helix chain 'D' and resid 289 through 299 Processing helix chain 'E' and resid 76 through 93 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA E 130 " --> pdb=" O PRO E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 164 " --> pdb=" O ARG E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.762A pdb=" N LEU E 178 " --> pdb=" O ALA E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER E 207 " --> pdb=" O HIS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 265 through 284 Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'F' and resid 76 through 93 Processing helix chain 'F' and resid 105 through 117 Processing helix chain 'F' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA F 130 " --> pdb=" O PRO F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 143 Processing helix chain 'F' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 164 " --> pdb=" O ARG F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU F 178 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 192 Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER F 207 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 225 Processing helix chain 'F' and resid 235 through 246 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 265 through 284 Processing helix chain 'F' and resid 289 through 299 Processing helix chain 'G' and resid 76 through 93 Processing helix chain 'G' and resid 105 through 117 Processing helix chain 'G' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA G 130 " --> pdb=" O PRO G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 143 Processing helix chain 'G' and resid 151 through 164 removed outlier: 3.711A pdb=" N LEU G 155 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU G 164 " --> pdb=" O ARG G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.762A pdb=" N LEU G 178 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 192 Processing helix chain 'G' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER G 207 " --> pdb=" O HIS G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 225 Processing helix chain 'G' and resid 235 through 246 Processing helix chain 'G' and resid 250 through 262 Processing helix chain 'G' and resid 265 through 284 Processing helix chain 'G' and resid 289 through 299 Processing helix chain 'H' and resid 76 through 93 Processing helix chain 'H' and resid 105 through 117 Processing helix chain 'H' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA H 130 " --> pdb=" O PRO H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 143 Processing helix chain 'H' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU H 155 " --> pdb=" O ARG H 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.963A pdb=" N LEU H 178 " --> pdb=" O ALA H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER H 207 " --> pdb=" O HIS H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 250 through 262 Processing helix chain 'H' and resid 265 through 284 Processing helix chain 'H' and resid 289 through 299 Processing helix chain 'I' and resid 76 through 93 Processing helix chain 'I' and resid 105 through 117 Processing helix chain 'I' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA I 130 " --> pdb=" O PRO I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 143 Processing helix chain 'I' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU I 155 " --> pdb=" O ARG I 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU I 164 " --> pdb=" O ARG I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU I 178 " --> pdb=" O ALA I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 192 Processing helix chain 'I' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 225 Processing helix chain 'I' and resid 235 through 246 Processing helix chain 'I' and resid 250 through 262 Processing helix chain 'I' and resid 265 through 284 Processing helix chain 'I' and resid 289 through 299 Processing helix chain 'J' and resid 76 through 93 Processing helix chain 'J' and resid 105 through 117 Processing helix chain 'J' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA J 130 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 143 Processing helix chain 'J' and resid 151 through 164 removed outlier: 3.711A pdb=" N LEU J 155 " --> pdb=" O ARG J 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU J 164 " --> pdb=" O ARG J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU J 178 " --> pdb=" O ALA J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 192 Processing helix chain 'J' and resid 203 through 208 removed outlier: 3.549A pdb=" N SER J 207 " --> pdb=" O HIS J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 225 Processing helix chain 'J' and resid 235 through 246 Processing helix chain 'J' and resid 250 through 262 Processing helix chain 'J' and resid 265 through 284 Processing helix chain 'J' and resid 289 through 299 Processing helix chain 'K' and resid 76 through 93 Processing helix chain 'K' and resid 105 through 117 Processing helix chain 'K' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA K 130 " --> pdb=" O PRO K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 143 Processing helix chain 'K' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU K 155 " --> pdb=" O ARG K 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU K 164 " --> pdb=" O ARG K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 178 removed outlier: 3.760A pdb=" N LEU K 178 " --> pdb=" O ALA K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 192 Processing helix chain 'K' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER K 207 " --> pdb=" O HIS K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 225 Processing helix chain 'K' and resid 235 through 246 Processing helix chain 'K' and resid 250 through 262 Processing helix chain 'K' and resid 265 through 284 Processing helix chain 'K' and resid 289 through 299 Processing helix chain 'L' and resid 76 through 93 Processing helix chain 'L' and resid 105 through 117 Processing helix chain 'L' and resid 126 through 130 removed outlier: 3.634A pdb=" N ALA L 130 " --> pdb=" O PRO L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU L 155 " --> pdb=" O ARG L 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU L 164 " --> pdb=" O ARG L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU L 178 " --> pdb=" O ALA L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 192 Processing helix chain 'L' and resid 203 through 208 removed outlier: 3.549A pdb=" N SER L 207 " --> pdb=" O HIS L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 225 Processing helix chain 'L' and resid 235 through 246 Processing helix chain 'L' and resid 250 through 262 Processing helix chain 'L' and resid 265 through 284 Processing helix chain 'L' and resid 289 through 299 Processing helix chain 'M' and resid 76 through 93 Processing helix chain 'M' and resid 105 through 117 Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA M 130 " --> pdb=" O PRO M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 143 Processing helix chain 'M' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU M 155 " --> pdb=" O ARG M 151 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU M 164 " --> pdb=" O ARG M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU M 178 " --> pdb=" O ALA M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 192 Processing helix chain 'M' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER M 207 " --> pdb=" O HIS M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 218 through 225 Processing helix chain 'M' and resid 235 through 246 Processing helix chain 'M' and resid 250 through 262 Processing helix chain 'M' and resid 265 through 284 Processing helix chain 'M' and resid 289 through 299 Processing helix chain 'N' and resid 76 through 93 Processing helix chain 'N' and resid 105 through 117 Processing helix chain 'N' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA N 130 " --> pdb=" O PRO N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 Processing helix chain 'N' and resid 151 through 164 removed outlier: 3.711A pdb=" N LEU N 155 " --> pdb=" O ARG N 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU N 178 " --> pdb=" O ALA N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 192 Processing helix chain 'N' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER N 207 " --> pdb=" O HIS N 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 225 Processing helix chain 'N' and resid 235 through 246 Processing helix chain 'N' and resid 250 through 262 Processing helix chain 'N' and resid 265 through 284 Processing helix chain 'N' and resid 289 through 299 Processing helix chain 'O' and resid 76 through 93 Processing helix chain 'O' and resid 105 through 117 Processing helix chain 'O' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA O 130 " --> pdb=" O PRO O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 143 Processing helix chain 'O' and resid 151 through 164 removed outlier: 3.711A pdb=" N LEU O 155 " --> pdb=" O ARG O 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU O 164 " --> pdb=" O ARG O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 178 removed outlier: 3.762A pdb=" N LEU O 178 " --> pdb=" O ALA O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 192 Processing helix chain 'O' and resid 203 through 208 removed outlier: 3.549A pdb=" N SER O 207 " --> pdb=" O HIS O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 218 through 225 Processing helix chain 'O' and resid 235 through 246 Processing helix chain 'O' and resid 250 through 262 Processing helix chain 'O' and resid 265 through 284 Processing helix chain 'O' and resid 289 through 299 Processing helix chain 'P' and resid 76 through 93 Processing helix chain 'P' and resid 105 through 117 Processing helix chain 'P' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA P 130 " --> pdb=" O PRO P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 143 Processing helix chain 'P' and resid 151 through 164 removed outlier: 3.712A pdb=" N LEU P 155 " --> pdb=" O ARG P 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU P 164 " --> pdb=" O ARG P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 178 removed outlier: 3.762A pdb=" N LEU P 178 " --> pdb=" O ALA P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 192 Processing helix chain 'P' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER P 207 " --> pdb=" O HIS P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 225 Processing helix chain 'P' and resid 235 through 246 Processing helix chain 'P' and resid 250 through 262 Processing helix chain 'P' and resid 265 through 284 Processing helix chain 'P' and resid 289 through 299 Processing helix chain 'Q' and resid 76 through 93 Processing helix chain 'Q' and resid 105 through 117 Processing helix chain 'Q' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA Q 130 " --> pdb=" O PRO Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 143 Processing helix chain 'Q' and resid 151 through 164 removed outlier: 3.711A pdb=" N LEU Q 155 " --> pdb=" O ARG Q 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU Q 164 " --> pdb=" O ARG Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 178 removed outlier: 3.762A pdb=" N LEU Q 178 " --> pdb=" O ALA Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 192 Processing helix chain 'Q' and resid 203 through 208 removed outlier: 3.549A pdb=" N SER Q 207 " --> pdb=" O HIS Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 218 through 225 Processing helix chain 'Q' and resid 235 through 246 Processing helix chain 'Q' and resid 250 through 262 Processing helix chain 'Q' and resid 265 through 284 Processing helix chain 'Q' and resid 289 through 299 Processing helix chain 'R' and resid 76 through 93 Processing helix chain 'R' and resid 105 through 117 Processing helix chain 'R' and resid 126 through 130 removed outlier: 3.635A pdb=" N ALA R 130 " --> pdb=" O PRO R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 Processing helix chain 'R' and resid 151 through 164 removed outlier: 3.711A pdb=" N LEU R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU R 164 " --> pdb=" O ARG R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 178 removed outlier: 3.761A pdb=" N LEU R 178 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 192 Processing helix chain 'R' and resid 203 through 208 removed outlier: 3.550A pdb=" N SER R 207 " --> pdb=" O HIS R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 225 Processing helix chain 'R' and resid 235 through 246 Processing helix chain 'R' and resid 250 through 262 Processing helix chain 'R' and resid 265 through 284 Processing helix chain 'R' and resid 289 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA A 96 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA B 96 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA C 96 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA D 96 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA E 96 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA F 96 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA G 96 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA H 96 " --> pdb=" O LEU H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA I 96 " --> pdb=" O LEU I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA J 96 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA K 96 " --> pdb=" O LEU K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA L 96 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA M 96 " --> pdb=" O LEU M 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA N 96 " --> pdb=" O LEU N 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 95 through 97 removed outlier: 6.292A pdb=" N ALA O 96 " --> pdb=" O LEU O 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA P 96 " --> pdb=" O LEU P 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA Q 96 " --> pdb=" O LEU Q 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 95 through 97 removed outlier: 6.291A pdb=" N ALA R 96 " --> pdb=" O LEU R 199 " (cutoff:3.500A) 1852 hydrogen bonds defined for protein. 5448 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: 6.09 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10271 1.33 - 1.45: 5489 1.45 - 1.58: 18242 1.58 - 1.70: 54 1.70 - 1.82: 270 Bond restraints: 34326 Sorted by residual: bond pdb=" C4 ADP G 401 " pdb=" C5 ADP G 401 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP K 401 " pdb=" C5 ADP K 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP J 401 " pdb=" C5 ADP J 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP Q 401 " pdb=" C5 ADP Q 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 34321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 43037 2.35 - 4.69: 2884 4.69 - 7.04: 342 7.04 - 9.38: 121 9.38 - 11.73: 38 Bond angle restraints: 46422 Sorted by residual: angle pdb=" N LYS O 80 " pdb=" CA LYS O 80 " pdb=" C LYS O 80 " ideal model delta sigma weight residual 111.14 106.08 5.06 1.08e+00 8.57e-01 2.20e+01 angle pdb=" N LYS R 80 " pdb=" CA LYS R 80 " pdb=" C LYS R 80 " ideal model delta sigma weight residual 111.14 106.20 4.94 1.08e+00 8.57e-01 2.09e+01 angle pdb=" N LYS G 80 " pdb=" CA LYS G 80 " pdb=" C LYS G 80 " ideal model delta sigma weight residual 111.14 106.27 4.87 1.08e+00 8.57e-01 2.03e+01 angle pdb=" N LYS P 80 " pdb=" CA LYS P 80 " pdb=" C LYS P 80 " ideal model delta sigma weight residual 111.14 106.30 4.84 1.08e+00 8.57e-01 2.01e+01 angle pdb=" N LYS I 80 " pdb=" CA LYS I 80 " pdb=" C LYS I 80 " ideal model delta sigma weight residual 111.14 106.31 4.83 1.08e+00 8.57e-01 2.00e+01 ... (remaining 46417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 20841 35.56 - 71.12: 205 71.12 - 106.69: 27 106.69 - 142.25: 32 142.25 - 177.81: 9 Dihedral angle restraints: 21114 sinusoidal: 8910 harmonic: 12204 Sorted by residual: dihedral pdb=" O1B ADP O 401 " pdb=" O3A ADP O 401 " pdb=" PB ADP O 401 " pdb=" PA ADP O 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.81 -177.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.44 176.56 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP N 401 " pdb=" O3A ADP N 401 " pdb=" PB ADP N 401 " pdb=" PA ADP N 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.79 -175.80 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 21111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3964 0.064 - 0.127: 1033 0.127 - 0.191: 295 0.191 - 0.255: 18 0.255 - 0.318: 36 Chirality restraints: 5346 Sorted by residual: chirality pdb=" CA ILE O 172 " pdb=" N ILE O 172 " pdb=" C ILE O 172 " pdb=" CB ILE O 172 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA ILE D 172 " pdb=" N ILE D 172 " pdb=" C ILE D 172 " pdb=" CB ILE D 172 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE Q 172 " pdb=" N ILE Q 172 " pdb=" C ILE Q 172 " pdb=" CB ILE Q 172 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 5343 not shown) Planarity restraints: 5940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 222 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C PHE G 222 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE G 222 " 0.019 2.00e-02 2.50e+03 pdb=" N SER G 223 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 222 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C PHE J 222 " 0.051 2.00e-02 2.50e+03 pdb=" O PHE J 222 " -0.019 2.00e-02 2.50e+03 pdb=" N SER J 223 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 222 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C PHE L 222 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE L 222 " -0.019 2.00e-02 2.50e+03 pdb=" N SER L 223 " -0.017 2.00e-02 2.50e+03 ... (remaining 5937 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3062 2.74 - 3.28: 34142 3.28 - 3.82: 57222 3.82 - 4.36: 66836 4.36 - 4.90: 108940 Nonbonded interactions: 270202 Sorted by model distance: nonbonded pdb=" O LEU J 189 " pdb=" OG1 THR J 193 " model vdw 2.197 3.040 nonbonded pdb=" O LEU E 189 " pdb=" OG1 THR E 193 " model vdw 2.197 3.040 nonbonded pdb=" O LEU P 189 " pdb=" OG1 THR P 193 " model vdw 2.197 3.040 nonbonded pdb=" O LEU K 189 " pdb=" OG1 THR K 193 " model vdw 2.198 3.040 nonbonded pdb=" O LEU D 189 " pdb=" OG1 THR D 193 " model vdw 2.198 3.040 ... (remaining 270197 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.930 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 34326 Z= 0.494 Angle : 1.310 11.728 46422 Z= 0.778 Chirality : 0.066 0.318 5346 Planarity : 0.007 0.046 5940 Dihedral : 13.362 177.811 13158 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 0.93 % Allowed : 3.62 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.57 (0.11), residues: 4158 helix: -1.61 (0.09), residues: 2376 sheet: -1.48 (0.21), residues: 540 loop : -1.52 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 220 TYR 0.015 0.002 TYR H 113 PHE 0.015 0.003 PHE H 141 TRP 0.014 0.003 TRP E 121 HIS 0.004 0.001 HIS P 282 Details of bonding type rmsd covalent geometry : bond 0.00871 (34326) covalent geometry : angle 1.31019 (46422) hydrogen bonds : bond 0.16081 ( 1852) hydrogen bonds : angle 7.12621 ( 5448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2010 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 1977 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 THR cc_start: 0.8868 (m) cc_final: 0.8590 (t) REVERT: A 160 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8034 (mtt180) REVERT: A 190 GLN cc_start: 0.8128 (pp30) cc_final: 0.7798 (pp30) REVERT: A 220 ARG cc_start: 0.8429 (ptp-170) cc_final: 0.7929 (ptm160) REVERT: A 232 ASN cc_start: 0.7392 (m-40) cc_final: 0.6954 (p0) REVERT: A 289 ASN cc_start: 0.9095 (p0) cc_final: 0.8578 (p0) REVERT: B 70 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7902 (Cg_exo) REVERT: B 78 THR cc_start: 0.8728 (m) cc_final: 0.8330 (t) REVERT: B 99 CYS cc_start: 0.6799 (p) cc_final: 0.6045 (m) REVERT: B 112 GLU cc_start: 0.7246 (tp30) cc_final: 0.6852 (tp30) REVERT: B 123 ILE cc_start: 0.9340 (pt) cc_final: 0.8904 (pt) REVERT: B 160 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8199 (mtt180) REVERT: B 220 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.7971 (ptm160) REVERT: B 227 LYS cc_start: 0.7887 (tttp) cc_final: 0.7172 (tppt) REVERT: C 169 LEU cc_start: 0.8268 (tp) cc_final: 0.7717 (tp) REVERT: C 173 ASP cc_start: 0.8100 (t0) cc_final: 0.7721 (p0) REVERT: C 220 ARG cc_start: 0.8041 (ptp-170) cc_final: 0.7718 (ttt180) REVERT: C 232 ASN cc_start: 0.7578 (m-40) cc_final: 0.6994 (p0) REVERT: C 289 ASN cc_start: 0.8927 (p0) cc_final: 0.8320 (m-40) REVERT: D 73 PHE cc_start: 0.6925 (t80) cc_final: 0.6672 (p90) REVERT: D 108 GLU cc_start: 0.7889 (tp30) cc_final: 0.7540 (tp30) REVERT: D 114 ARG cc_start: 0.9004 (ttp-170) cc_final: 0.8315 (ttp-170) REVERT: D 122 MET cc_start: 0.8543 (ttt) cc_final: 0.8166 (ttp) REVERT: D 169 LEU cc_start: 0.8791 (tp) cc_final: 0.8324 (tp) REVERT: D 220 ARG cc_start: 0.8012 (ptp-170) cc_final: 0.7321 (ttt180) REVERT: D 227 LYS cc_start: 0.7955 (tttp) cc_final: 0.7159 (tppt) REVERT: D 232 ASN cc_start: 0.7387 (m-40) cc_final: 0.6966 (p0) REVERT: D 258 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8811 (tp-100) REVERT: D 259 GLN cc_start: 0.9250 (mt0) cc_final: 0.8978 (pt0) REVERT: D 289 ASN cc_start: 0.8956 (p0) cc_final: 0.7887 (m-40) REVERT: E 99 CYS cc_start: 0.6782 (p) cc_final: 0.6159 (m) REVERT: E 220 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.7994 (ptm160) REVERT: E 289 ASN cc_start: 0.9010 (p0) cc_final: 0.8359 (p0) REVERT: E 297 PHE cc_start: 0.7382 (t80) cc_final: 0.6674 (t80) REVERT: F 99 CYS cc_start: 0.7152 (p) cc_final: 0.6388 (m) REVERT: F 160 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8183 (mtt180) REVERT: F 173 ASP cc_start: 0.8016 (t0) cc_final: 0.7762 (p0) REVERT: F 205 VAL cc_start: 0.6949 (t) cc_final: 0.6216 (t) REVERT: F 209 MET cc_start: 0.2208 (mtt) cc_final: 0.1685 (mtp) REVERT: F 220 ARG cc_start: 0.8320 (ptp-170) cc_final: 0.8070 (ptm160) REVERT: F 289 ASN cc_start: 0.9013 (p0) cc_final: 0.8508 (p0) REVERT: F 297 PHE cc_start: 0.7330 (t80) cc_final: 0.6758 (t80) REVERT: G 78 THR cc_start: 0.8873 (m) cc_final: 0.8272 (t) REVERT: G 112 GLU cc_start: 0.7251 (tp30) cc_final: 0.6790 (tp30) REVERT: G 155 LEU cc_start: 0.8760 (tp) cc_final: 0.8556 (tp) REVERT: G 160 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8076 (mtt180) REVERT: G 220 ARG cc_start: 0.8545 (ptp-170) cc_final: 0.7979 (ptm160) REVERT: G 232 ASN cc_start: 0.7326 (m-40) cc_final: 0.6982 (p0) REVERT: G 279 MET cc_start: 0.8719 (ttm) cc_final: 0.8461 (ptt) REVERT: G 297 PHE cc_start: 0.7173 (t80) cc_final: 0.6443 (t80) REVERT: H 99 CYS cc_start: 0.6509 (p) cc_final: 0.5786 (m) REVERT: H 169 LEU cc_start: 0.8485 (tp) cc_final: 0.8101 (tp) REVERT: H 186 LEU cc_start: 0.9455 (mp) cc_final: 0.9212 (mt) REVERT: H 209 MET cc_start: 0.2368 (mtt) cc_final: 0.2050 (mtp) REVERT: H 220 ARG cc_start: 0.8296 (ptp-170) cc_final: 0.8081 (ptm160) REVERT: H 232 ASN cc_start: 0.7262 (m-40) cc_final: 0.6840 (p0) REVERT: H 271 ASN cc_start: 0.9058 (t0) cc_final: 0.8653 (t0) REVERT: H 289 ASN cc_start: 0.9034 (p0) cc_final: 0.8469 (p0) REVERT: I 112 GLU cc_start: 0.7178 (tp30) cc_final: 0.6698 (tp30) REVERT: I 123 ILE cc_start: 0.9411 (pt) cc_final: 0.8762 (pt) REVERT: I 160 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8132 (mtt180) REVERT: I 169 LEU cc_start: 0.8773 (tp) cc_final: 0.8287 (tp) REVERT: I 220 ARG cc_start: 0.8318 (ptp-170) cc_final: 0.7902 (ptm160) REVERT: I 227 LYS cc_start: 0.7934 (tttp) cc_final: 0.7611 (tppt) REVERT: I 232 ASN cc_start: 0.7487 (m-40) cc_final: 0.6989 (p0) REVERT: I 269 ILE cc_start: 0.9097 (mm) cc_final: 0.8874 (tp) REVERT: I 271 ASN cc_start: 0.8946 (t0) cc_final: 0.8530 (t0) REVERT: J 112 GLU cc_start: 0.7168 (tp30) cc_final: 0.6741 (tp30) REVERT: J 142 GLU cc_start: 0.8145 (tp30) cc_final: 0.7875 (tp30) REVERT: J 157 ARG cc_start: 0.6337 (mpp80) cc_final: 0.6010 (mtt180) REVERT: J 160 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8070 (mtt180) REVERT: J 169 LEU cc_start: 0.8685 (tp) cc_final: 0.8296 (tp) REVERT: J 220 ARG cc_start: 0.8354 (ptp-170) cc_final: 0.7889 (ptm160) REVERT: J 232 ASN cc_start: 0.7387 (m-40) cc_final: 0.7071 (p0) REVERT: J 271 ASN cc_start: 0.8982 (t0) cc_final: 0.8215 (p0) REVERT: J 289 ASN cc_start: 0.9056 (p0) cc_final: 0.8552 (p0) REVERT: K 78 THR cc_start: 0.8922 (m) cc_final: 0.8507 (t) REVERT: K 112 GLU cc_start: 0.7277 (tp30) cc_final: 0.6959 (tp30) REVERT: K 123 ILE cc_start: 0.9408 (pt) cc_final: 0.9134 (pt) REVERT: K 169 LEU cc_start: 0.8537 (tp) cc_final: 0.8144 (tp) REVERT: K 186 LEU cc_start: 0.9437 (mp) cc_final: 0.9190 (mt) REVERT: K 220 ARG cc_start: 0.8366 (ptp-170) cc_final: 0.7863 (ptm160) REVERT: K 232 ASN cc_start: 0.7259 (m-40) cc_final: 0.6875 (p0) REVERT: K 289 ASN cc_start: 0.9066 (p0) cc_final: 0.8419 (p0) REVERT: K 297 PHE cc_start: 0.7312 (t80) cc_final: 0.6380 (t80) REVERT: L 112 GLU cc_start: 0.7143 (tp30) cc_final: 0.6654 (tp30) REVERT: L 123 ILE cc_start: 0.9397 (pt) cc_final: 0.8602 (pt) REVERT: L 157 ARG cc_start: 0.6657 (mpp80) cc_final: 0.6252 (mtt90) REVERT: L 160 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8200 (mtt180) REVERT: L 169 LEU cc_start: 0.8674 (tp) cc_final: 0.8292 (tp) REVERT: L 220 ARG cc_start: 0.8541 (ptp-170) cc_final: 0.7926 (ptm160) REVERT: L 232 ASN cc_start: 0.7504 (m-40) cc_final: 0.6931 (p0) REVERT: L 271 ASN cc_start: 0.8996 (t0) cc_final: 0.8683 (t0) REVERT: M 78 THR cc_start: 0.8893 (m) cc_final: 0.8473 (t) REVERT: M 108 GLU cc_start: 0.8003 (tp30) cc_final: 0.7637 (tp30) REVERT: M 124 THR cc_start: 0.9333 (p) cc_final: 0.9133 (p) REVERT: M 142 GLU cc_start: 0.8223 (tp30) cc_final: 0.7985 (tp30) REVERT: M 160 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8258 (mtt90) REVERT: M 169 LEU cc_start: 0.8756 (tp) cc_final: 0.8425 (tp) REVERT: M 173 ASP cc_start: 0.8080 (t0) cc_final: 0.7608 (p0) REVERT: M 209 MET cc_start: 0.2893 (mtt) cc_final: 0.2687 (mtp) REVERT: M 220 ARG cc_start: 0.8233 (ptp-170) cc_final: 0.7700 (ptm160) REVERT: M 232 ASN cc_start: 0.7378 (m-40) cc_final: 0.6956 (p0) REVERT: M 271 ASN cc_start: 0.8959 (t0) cc_final: 0.8404 (p0) REVERT: M 289 ASN cc_start: 0.8967 (p0) cc_final: 0.8278 (p0) REVERT: M 297 PHE cc_start: 0.6862 (t80) cc_final: 0.6096 (t80) REVERT: N 78 THR cc_start: 0.8975 (m) cc_final: 0.8563 (t) REVERT: N 122 MET cc_start: 0.8343 (ttt) cc_final: 0.8058 (tmm) REVERT: N 123 ILE cc_start: 0.9323 (pt) cc_final: 0.8562 (pt) REVERT: N 160 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8010 (mtt180) REVERT: N 186 LEU cc_start: 0.9494 (mp) cc_final: 0.9293 (mt) REVERT: N 209 MET cc_start: 0.2479 (mtt) cc_final: 0.2255 (mtp) REVERT: N 220 ARG cc_start: 0.8175 (ptp-170) cc_final: 0.7921 (ptm160) REVERT: N 258 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8743 (tp-100) REVERT: N 267 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8127 (mm) REVERT: O 78 THR cc_start: 0.8953 (m) cc_final: 0.8483 (t) REVERT: O 108 GLU cc_start: 0.7816 (tp30) cc_final: 0.7608 (tp30) REVERT: O 160 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8073 (mtt180) REVERT: O 169 LEU cc_start: 0.8767 (tp) cc_final: 0.8413 (tp) REVERT: O 181 GLU cc_start: 0.9151 (tt0) cc_final: 0.8414 (pm20) REVERT: O 182 VAL cc_start: 0.8570 (t) cc_final: 0.7908 (t) REVERT: O 220 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7533 (ptm160) REVERT: O 267 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7858 (mm) REVERT: O 297 PHE cc_start: 0.6896 (t80) cc_final: 0.6273 (t80) REVERT: P 108 GLU cc_start: 0.7874 (tp30) cc_final: 0.7572 (tp30) REVERT: P 143 LEU cc_start: 0.8901 (mt) cc_final: 0.8595 (mt) REVERT: P 169 LEU cc_start: 0.8804 (tp) cc_final: 0.8550 (tp) REVERT: P 174 GLU cc_start: 0.6800 (mp0) cc_final: 0.6403 (mp0) REVERT: P 220 ARG cc_start: 0.8141 (ptp-170) cc_final: 0.7789 (ptm160) REVERT: P 232 ASN cc_start: 0.7185 (m-40) cc_final: 0.6895 (p0) REVERT: P 267 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7899 (mt) REVERT: P 268 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7767 (mtt-85) REVERT: P 269 ILE cc_start: 0.8941 (mm) cc_final: 0.8703 (tp) REVERT: P 289 ASN cc_start: 0.8965 (p0) cc_final: 0.8765 (p0) REVERT: Q 99 CYS cc_start: 0.6779 (p) cc_final: 0.6239 (m) REVERT: Q 108 GLU cc_start: 0.7911 (tp30) cc_final: 0.7571 (tp30) REVERT: Q 123 ILE cc_start: 0.9445 (pt) cc_final: 0.9235 (pt) REVERT: Q 160 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8041 (mtt180) REVERT: Q 169 LEU cc_start: 0.8658 (tp) cc_final: 0.8211 (tp) REVERT: Q 186 LEU cc_start: 0.9470 (mp) cc_final: 0.9233 (mt) REVERT: Q 220 ARG cc_start: 0.8446 (ptp-170) cc_final: 0.7880 (ptm160) REVERT: Q 271 ASN cc_start: 0.8991 (t0) cc_final: 0.8603 (t0) REVERT: Q 289 ASN cc_start: 0.9014 (p0) cc_final: 0.8389 (p0) REVERT: R 78 THR cc_start: 0.9023 (m) cc_final: 0.8505 (t) REVERT: R 123 ILE cc_start: 0.9375 (pt) cc_final: 0.9080 (pt) REVERT: R 160 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8181 (mtt180) REVERT: R 169 LEU cc_start: 0.8730 (tp) cc_final: 0.8369 (tp) REVERT: R 220 ARG cc_start: 0.8244 (ptp-170) cc_final: 0.7755 (ptm160) REVERT: R 232 ASN cc_start: 0.7336 (m-40) cc_final: 0.6576 (p0) REVERT: R 267 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7885 (mm) outliers start: 33 outliers final: 13 residues processed: 1981 average time/residue: 0.2496 time to fit residues: 740.9933 Evaluate side-chains 1233 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1215 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 119 ASN A 146 ASN A 258 GLN A 262 GLN B 81 GLN B 146 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 262 GLN C 81 GLN C 146 ASN C 167 GLN C 258 GLN C 262 GLN D 81 GLN D 167 GLN D 258 GLN D 262 GLN D 272 HIS ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 146 ASN E 258 GLN E 262 GLN F 81 GLN F 146 ASN F 258 GLN F 262 GLN G 81 GLN G 146 ASN G 258 GLN G 262 GLN ** G 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 146 ASN H 258 GLN H 262 GLN H 272 HIS I 81 GLN I 258 GLN I 262 GLN J 81 GLN J 146 ASN J 167 GLN J 258 GLN J 262 GLN K 81 GLN K 119 ASN K 258 GLN K 262 GLN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN L 146 ASN L 258 GLN L 262 GLN M 81 GLN M 167 GLN M 258 GLN M 262 GLN N 81 GLN N 146 ASN ** N 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 258 GLN N 262 GLN ** N 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN O 117 ASN ** O 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 258 GLN O 262 GLN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 272 HIS P 81 GLN P 258 GLN P 262 GLN ** P 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN Q 119 ASN ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 258 GLN Q 262 GLN R 81 GLN R 117 ASN R 146 ASN ** R 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 GLN R 262 GLN ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 272 HIS Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.173287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138337 restraints weight = 64562.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.143311 restraints weight = 42340.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.146998 restraints weight = 30739.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149684 restraints weight = 23961.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.151658 restraints weight = 19721.113| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34326 Z= 0.168 Angle : 0.750 9.676 46422 Z= 0.366 Chirality : 0.044 0.186 5346 Planarity : 0.006 0.079 5940 Dihedral : 12.656 176.453 4842 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.36 % Allowed : 3.34 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.12), residues: 4158 helix: -0.40 (0.10), residues: 2502 sheet: -1.57 (0.20), residues: 594 loop : -0.73 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 268 TYR 0.022 0.002 TYR D 292 PHE 0.016 0.002 PHE E 141 TRP 0.015 0.001 TRP B 246 HIS 0.004 0.001 HIS N 177 Details of bonding type rmsd covalent geometry : bond 0.00363 (34326) covalent geometry : angle 0.75000 (46422) hydrogen bonds : bond 0.03751 ( 1852) hydrogen bonds : angle 4.98810 ( 5448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1549 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.9239 (pt) cc_final: 0.8989 (pt) REVERT: A 220 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7643 (ptm160) REVERT: A 232 ASN cc_start: 0.7284 (m-40) cc_final: 0.6734 (p0) REVERT: A 233 LYS cc_start: 0.8287 (tppp) cc_final: 0.7696 (tppp) REVERT: A 236 LYS cc_start: 0.8740 (tptp) cc_final: 0.8343 (tppt) REVERT: A 251 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7364 (tm-30) REVERT: A 259 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8821 (pm20) REVERT: A 289 ASN cc_start: 0.8538 (p0) cc_final: 0.7631 (p0) REVERT: B 73 PHE cc_start: 0.7430 (t80) cc_final: 0.5196 (t80) REVERT: B 78 THR cc_start: 0.8524 (m) cc_final: 0.7874 (m) REVERT: B 116 THR cc_start: 0.8159 (p) cc_final: 0.7957 (t) REVERT: B 122 MET cc_start: 0.7805 (tmm) cc_final: 0.7332 (tmm) REVERT: B 143 LEU cc_start: 0.9383 (mt) cc_final: 0.8813 (mt) REVERT: B 155 LEU cc_start: 0.8822 (tp) cc_final: 0.8615 (tp) REVERT: B 190 GLN cc_start: 0.8255 (pt0) cc_final: 0.7935 (pt0) REVERT: B 259 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8887 (pm20) REVERT: B 267 LEU cc_start: 0.8537 (mm) cc_final: 0.8316 (mt) REVERT: B 289 ASN cc_start: 0.8892 (p0) cc_final: 0.8428 (p0) REVERT: C 136 LEU cc_start: 0.9150 (mt) cc_final: 0.8933 (mm) REVERT: C 142 GLU cc_start: 0.8195 (tp30) cc_final: 0.7967 (tp30) REVERT: C 155 LEU cc_start: 0.8935 (tp) cc_final: 0.8713 (tp) REVERT: C 173 ASP cc_start: 0.8359 (t0) cc_final: 0.8091 (m-30) REVERT: C 232 ASN cc_start: 0.7451 (m-40) cc_final: 0.6807 (p0) REVERT: C 233 LYS cc_start: 0.8286 (tppp) cc_final: 0.7796 (tppp) REVERT: C 258 GLN cc_start: 0.9042 (tp40) cc_final: 0.8770 (tp40) REVERT: C 259 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: C 271 ASN cc_start: 0.8688 (t0) cc_final: 0.7934 (p0) REVERT: D 120 VAL cc_start: 0.9248 (t) cc_final: 0.8915 (m) REVERT: D 135 CYS cc_start: 0.8438 (m) cc_final: 0.8197 (m) REVERT: D 145 MET cc_start: 0.7132 (mpp) cc_final: 0.6658 (mpp) REVERT: D 160 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8132 (mtt90) REVERT: D 232 ASN cc_start: 0.7342 (m-40) cc_final: 0.6757 (p0) REVERT: D 233 LYS cc_start: 0.8304 (tppp) cc_final: 0.7593 (tptm) REVERT: D 252 LYS cc_start: 0.8473 (ptpp) cc_final: 0.7700 (tppt) REVERT: D 258 GLN cc_start: 0.9118 (tp40) cc_final: 0.8758 (tp40) REVERT: D 263 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7517 (mtmt) REVERT: D 267 LEU cc_start: 0.8601 (mm) cc_final: 0.8072 (mt) REVERT: D 269 ILE cc_start: 0.8785 (tp) cc_final: 0.8560 (pt) REVERT: D 271 ASN cc_start: 0.8782 (t0) cc_final: 0.7965 (p0) REVERT: E 143 LEU cc_start: 0.9440 (mt) cc_final: 0.8939 (mt) REVERT: E 155 LEU cc_start: 0.8845 (tp) cc_final: 0.8627 (tp) REVERT: E 258 GLN cc_start: 0.9023 (tp40) cc_final: 0.8524 (tp-100) REVERT: E 271 ASN cc_start: 0.8726 (t0) cc_final: 0.8414 (t0) REVERT: E 289 ASN cc_start: 0.8424 (p0) cc_final: 0.7189 (p0) REVERT: F 73 PHE cc_start: 0.7507 (t80) cc_final: 0.6748 (t80) REVERT: F 81 GLN cc_start: 0.8791 (tm130) cc_final: 0.8352 (pt0) REVERT: F 209 MET cc_start: 0.2213 (mtt) cc_final: 0.1375 (mtp) REVERT: F 233 LYS cc_start: 0.7877 (tppp) cc_final: 0.7601 (tptt) REVERT: F 258 GLN cc_start: 0.9149 (tp40) cc_final: 0.8731 (tp-100) REVERT: F 271 ASN cc_start: 0.8780 (t0) cc_final: 0.8550 (t0) REVERT: F 289 ASN cc_start: 0.8721 (p0) cc_final: 0.7662 (p0) REVERT: G 73 PHE cc_start: 0.7513 (t80) cc_final: 0.6270 (t80) REVERT: G 78 THR cc_start: 0.8646 (m) cc_final: 0.8163 (m) REVERT: G 83 TRP cc_start: 0.7425 (m-10) cc_final: 0.6801 (m-10) REVERT: G 86 MET cc_start: 0.7399 (tpp) cc_final: 0.7006 (ttm) REVERT: G 108 GLU cc_start: 0.7568 (tp30) cc_final: 0.7332 (tp30) REVERT: G 112 GLU cc_start: 0.7125 (tp30) cc_final: 0.6767 (tp30) REVERT: G 122 MET cc_start: 0.8387 (ttt) cc_final: 0.8153 (tmm) REVERT: G 143 LEU cc_start: 0.9309 (mt) cc_final: 0.9029 (mt) REVERT: G 232 ASN cc_start: 0.7256 (m-40) cc_final: 0.6982 (p0) REVERT: G 233 LYS cc_start: 0.8207 (tppp) cc_final: 0.7546 (mmmm) REVERT: G 236 LYS cc_start: 0.8624 (tptp) cc_final: 0.8418 (tppt) REVERT: G 251 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7258 (tm-30) REVERT: G 289 ASN cc_start: 0.9031 (p0) cc_final: 0.7137 (p0) REVERT: G 291 ASP cc_start: 0.9163 (t0) cc_final: 0.8641 (p0) REVERT: G 292 TYR cc_start: 0.8507 (m-10) cc_final: 0.8181 (m-10) REVERT: H 145 MET cc_start: 0.6910 (mpp) cc_final: 0.6365 (mpp) REVERT: H 209 MET cc_start: 0.2409 (mtt) cc_final: 0.1746 (mtp) REVERT: H 232 ASN cc_start: 0.7174 (m-40) cc_final: 0.6764 (p0) REVERT: H 233 LYS cc_start: 0.8322 (tppp) cc_final: 0.7776 (mmmm) REVERT: H 251 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7526 (tm-30) REVERT: H 252 LYS cc_start: 0.8439 (ptpp) cc_final: 0.7946 (tppt) REVERT: H 258 GLN cc_start: 0.9113 (tp40) cc_final: 0.8728 (tp40) REVERT: H 259 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: H 271 ASN cc_start: 0.8802 (t0) cc_final: 0.8433 (t0) REVERT: H 289 ASN cc_start: 0.8581 (p0) cc_final: 0.7452 (p0) REVERT: I 73 PHE cc_start: 0.7539 (t80) cc_final: 0.5916 (t80) REVERT: I 86 MET cc_start: 0.7234 (tpp) cc_final: 0.6952 (ttm) REVERT: I 108 GLU cc_start: 0.7517 (tp30) cc_final: 0.7247 (tp30) REVERT: I 145 MET cc_start: 0.7097 (mpp) cc_final: 0.6725 (mpp) REVERT: I 232 ASN cc_start: 0.7271 (m-40) cc_final: 0.6831 (p0) REVERT: I 233 LYS cc_start: 0.8290 (tppp) cc_final: 0.7858 (tppp) REVERT: I 251 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7307 (tm-30) REVERT: I 258 GLN cc_start: 0.9029 (tp40) cc_final: 0.8724 (tp40) REVERT: I 289 ASN cc_start: 0.9000 (p0) cc_final: 0.8605 (p0) REVERT: J 73 PHE cc_start: 0.7598 (t80) cc_final: 0.5860 (t80) REVERT: J 86 MET cc_start: 0.7268 (tpp) cc_final: 0.6789 (ttm) REVERT: J 108 GLU cc_start: 0.7484 (tp30) cc_final: 0.7165 (tp30) REVERT: J 120 VAL cc_start: 0.9212 (t) cc_final: 0.8969 (m) REVERT: J 142 GLU cc_start: 0.8136 (tp30) cc_final: 0.7784 (tp30) REVERT: J 145 MET cc_start: 0.6939 (mpp) cc_final: 0.6552 (mpp) REVERT: J 160 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8105 (ttm170) REVERT: J 220 ARG cc_start: 0.8217 (ptp-170) cc_final: 0.7980 (mtp180) REVERT: J 232 ASN cc_start: 0.7260 (m-40) cc_final: 0.7048 (p0) REVERT: J 233 LYS cc_start: 0.8381 (tppp) cc_final: 0.7625 (mmmm) REVERT: J 251 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7054 (tm-30) REVERT: K 73 PHE cc_start: 0.7416 (t80) cc_final: 0.5909 (t80) REVERT: K 78 THR cc_start: 0.8613 (m) cc_final: 0.8101 (m) REVERT: K 108 GLU cc_start: 0.7579 (tp30) cc_final: 0.7172 (tp30) REVERT: K 122 MET cc_start: 0.7502 (tmm) cc_final: 0.7096 (tmm) REVERT: K 136 LEU cc_start: 0.9257 (mt) cc_final: 0.9040 (mm) REVERT: K 145 MET cc_start: 0.6973 (mpp) cc_final: 0.6471 (mpp) REVERT: K 155 LEU cc_start: 0.8857 (tp) cc_final: 0.8629 (tp) REVERT: K 232 ASN cc_start: 0.7288 (m-40) cc_final: 0.6901 (p0) REVERT: K 233 LYS cc_start: 0.8331 (tppp) cc_final: 0.7712 (mmmm) REVERT: K 251 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7427 (tm-30) REVERT: K 258 GLN cc_start: 0.9080 (tp40) cc_final: 0.8714 (tp40) REVERT: L 86 MET cc_start: 0.7302 (tpp) cc_final: 0.6926 (ttm) REVERT: L 112 GLU cc_start: 0.7294 (tp30) cc_final: 0.6802 (tp30) REVERT: L 136 LEU cc_start: 0.9260 (mt) cc_final: 0.9041 (mm) REVERT: L 145 MET cc_start: 0.6971 (mpp) cc_final: 0.6557 (mpp) REVERT: L 232 ASN cc_start: 0.7434 (m-40) cc_final: 0.6896 (p0) REVERT: L 233 LYS cc_start: 0.8399 (tppp) cc_final: 0.7904 (tppp) REVERT: L 251 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7692 (tm-30) REVERT: L 258 GLN cc_start: 0.8966 (tp40) cc_final: 0.8749 (tp40) REVERT: L 259 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8954 (pm20) REVERT: L 289 ASN cc_start: 0.8344 (p0) cc_final: 0.8009 (p0) REVERT: M 80 LYS cc_start: 0.9004 (mttt) cc_final: 0.8702 (mttp) REVERT: M 86 MET cc_start: 0.7360 (tpp) cc_final: 0.6994 (ttm) REVERT: M 112 GLU cc_start: 0.8289 (pt0) cc_final: 0.7908 (pt0) REVERT: M 136 LEU cc_start: 0.9291 (mt) cc_final: 0.9000 (mm) REVERT: M 145 MET cc_start: 0.6746 (mpp) cc_final: 0.6343 (mpp) REVERT: M 160 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8162 (ttm170) REVERT: M 209 MET cc_start: 0.2550 (mtt) cc_final: 0.1927 (mtp) REVERT: M 232 ASN cc_start: 0.7115 (m-40) cc_final: 0.6894 (p0) REVERT: M 233 LYS cc_start: 0.8079 (tppp) cc_final: 0.7518 (mmmm) REVERT: M 251 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7232 (tm-30) REVERT: M 258 GLN cc_start: 0.9021 (tp40) cc_final: 0.8770 (mm-40) REVERT: M 259 GLN cc_start: 0.9443 (pt0) cc_final: 0.9202 (tm-30) REVERT: M 269 ILE cc_start: 0.8780 (mm) cc_final: 0.8495 (tp) REVERT: M 271 ASN cc_start: 0.8874 (t0) cc_final: 0.8591 (p0) REVERT: N 81 GLN cc_start: 0.8751 (tm130) cc_final: 0.8306 (pt0) REVERT: N 209 MET cc_start: 0.2349 (mtt) cc_final: 0.1507 (mtp) REVERT: N 232 ASN cc_start: 0.7137 (m-40) cc_final: 0.6590 (p0) REVERT: N 240 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8406 (ttpt) REVERT: N 251 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7381 (tm-30) REVERT: N 258 GLN cc_start: 0.9138 (tp40) cc_final: 0.8657 (tp-100) REVERT: N 263 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7572 (mtmt) REVERT: N 289 ASN cc_start: 0.9034 (p0) cc_final: 0.8195 (p0) REVERT: O 86 MET cc_start: 0.7169 (tpp) cc_final: 0.6607 (ttm) REVERT: O 112 GLU cc_start: 0.8497 (pt0) cc_final: 0.7901 (pt0) REVERT: O 135 CYS cc_start: 0.8489 (m) cc_final: 0.8289 (m) REVERT: O 145 MET cc_start: 0.7149 (mpp) cc_final: 0.6517 (mpp) REVERT: O 155 LEU cc_start: 0.8732 (tp) cc_final: 0.8526 (tp) REVERT: O 160 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8069 (ttm170) REVERT: O 181 GLU cc_start: 0.9060 (tt0) cc_final: 0.8375 (pm20) REVERT: O 182 VAL cc_start: 0.8443 (t) cc_final: 0.7562 (t) REVERT: O 220 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7602 (ptm160) REVERT: O 251 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7194 (tm-30) REVERT: O 258 GLN cc_start: 0.9123 (tp40) cc_final: 0.8753 (tp40) REVERT: O 289 ASN cc_start: 0.9055 (p0) cc_final: 0.8137 (p0) REVERT: P 80 LYS cc_start: 0.9003 (mttt) cc_final: 0.8780 (mttp) REVERT: P 143 LEU cc_start: 0.9260 (mt) cc_final: 0.9035 (mt) REVERT: P 145 MET cc_start: 0.6750 (mpp) cc_final: 0.6254 (mpp) REVERT: P 155 LEU cc_start: 0.8831 (tp) cc_final: 0.8605 (tp) REVERT: P 169 LEU cc_start: 0.8902 (tp) cc_final: 0.8318 (tp) REVERT: P 173 ASP cc_start: 0.8253 (t70) cc_final: 0.8052 (t0) REVERT: P 232 ASN cc_start: 0.7059 (m-40) cc_final: 0.6750 (p0) REVERT: P 233 LYS cc_start: 0.8205 (tppp) cc_final: 0.7719 (tppp) REVERT: P 235 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8814 (mmtt) REVERT: P 251 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7328 (tm-30) REVERT: P 258 GLN cc_start: 0.9060 (tp40) cc_final: 0.8633 (tp40) REVERT: P 259 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8714 (pm20) REVERT: P 289 ASN cc_start: 0.8646 (p0) cc_final: 0.7954 (p0) REVERT: Q 135 CYS cc_start: 0.8469 (m) cc_final: 0.8231 (m) REVERT: Q 143 LEU cc_start: 0.9368 (mt) cc_final: 0.9003 (mt) REVERT: Q 145 MET cc_start: 0.6980 (mpp) cc_final: 0.6386 (mpp) REVERT: Q 220 ARG cc_start: 0.8173 (ptp-170) cc_final: 0.7830 (ptm160) REVERT: Q 232 ASN cc_start: 0.7308 (m-40) cc_final: 0.6814 (p0) REVERT: Q 233 LYS cc_start: 0.8264 (tppp) cc_final: 0.7699 (tppp) REVERT: Q 236 LYS cc_start: 0.8729 (tptp) cc_final: 0.8460 (tppt) REVERT: Q 240 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8540 (ttpt) REVERT: Q 251 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7276 (tm-30) REVERT: Q 271 ASN cc_start: 0.8892 (t0) cc_final: 0.8631 (t0) REVERT: R 86 MET cc_start: 0.7520 (tpp) cc_final: 0.6698 (ttm) REVERT: R 112 GLU cc_start: 0.8392 (pt0) cc_final: 0.8168 (mt-10) REVERT: R 136 LEU cc_start: 0.9255 (mt) cc_final: 0.9029 (mt) REVERT: R 174 GLU cc_start: 0.7197 (mp0) cc_final: 0.6730 (mp0) REVERT: R 232 ASN cc_start: 0.7239 (m-40) cc_final: 0.6705 (p0) REVERT: R 251 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7595 (tm-30) REVERT: R 252 LYS cc_start: 0.8528 (ptpp) cc_final: 0.7934 (tppt) REVERT: R 258 GLN cc_start: 0.9058 (tp40) cc_final: 0.8690 (tp40) REVERT: R 289 ASN cc_start: 0.9056 (p0) cc_final: 0.8579 (p0) outliers start: 13 outliers final: 1 residues processed: 1550 average time/residue: 0.2249 time to fit residues: 538.6790 Evaluate side-chains 1180 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1173 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 225 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 300 optimal weight: 0.0770 chunk 3 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 329 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 119 ASN A 146 ASN A 167 GLN B 77 GLN B 81 GLN B 146 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 262 GLN C 81 GLN C 146 ASN D 81 GLN D 117 ASN D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN F 81 GLN F 146 ASN G 81 GLN G 295 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 146 ASN H 272 HIS ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN J 81 GLN ** J 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN K 146 ASN L 81 GLN L 271 ASN M 81 GLN M 117 ASN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 ASN N 81 GLN N 146 ASN N 271 ASN N 272 HIS O 81 GLN O 146 ASN O 259 GLN O 272 HIS P 81 GLN ** P 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN Q 117 ASN ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 ASN ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 GLN R 146 ASN ** R 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.170955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135832 restraints weight = 64774.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140766 restraints weight = 42212.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144297 restraints weight = 30548.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146883 restraints weight = 23975.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148765 restraints weight = 19902.396| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34326 Z= 0.181 Angle : 0.769 9.719 46422 Z= 0.368 Chirality : 0.044 0.256 5346 Planarity : 0.006 0.144 5940 Dihedral : 12.247 174.888 4842 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.17 % Allowed : 3.45 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4158 helix: 0.04 (0.10), residues: 2484 sheet: -1.46 (0.20), residues: 630 loop : -0.32 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 194 TYR 0.022 0.001 TYR F 292 PHE 0.019 0.002 PHE M 141 TRP 0.034 0.002 TRP G 246 HIS 0.007 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00378 (34326) covalent geometry : angle 0.76946 (46422) hydrogen bonds : bond 0.03537 ( 1852) hydrogen bonds : angle 4.66034 ( 5448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1330 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 CYS cc_start: 0.8316 (m) cc_final: 0.8080 (m) REVERT: A 169 LEU cc_start: 0.8537 (tp) cc_final: 0.8273 (tp) REVERT: A 174 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 232 ASN cc_start: 0.7265 (m-40) cc_final: 0.6694 (p0) REVERT: A 233 LYS cc_start: 0.8281 (tppp) cc_final: 0.7749 (tppp) REVERT: A 240 LYS cc_start: 0.8791 (mttt) cc_final: 0.8552 (mttm) REVERT: A 251 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7730 (tm-30) REVERT: A 252 LYS cc_start: 0.8531 (ptpp) cc_final: 0.7697 (tppt) REVERT: A 258 GLN cc_start: 0.9087 (tp40) cc_final: 0.8523 (tp40) REVERT: A 259 GLN cc_start: 0.9093 (pm20) cc_final: 0.8839 (pm20) REVERT: A 270 LEU cc_start: 0.9252 (tt) cc_final: 0.8875 (pp) REVERT: B 78 THR cc_start: 0.8078 (m) cc_final: 0.7821 (m) REVERT: B 143 LEU cc_start: 0.9365 (mt) cc_final: 0.8941 (mt) REVERT: B 145 MET cc_start: 0.7078 (mpp) cc_final: 0.6599 (mpp) REVERT: B 169 LEU cc_start: 0.8477 (tp) cc_final: 0.8204 (tp) REVERT: B 182 VAL cc_start: 0.8132 (t) cc_final: 0.7906 (t) REVERT: B 190 GLN cc_start: 0.8622 (pt0) cc_final: 0.8195 (pt0) REVERT: B 232 ASN cc_start: 0.7360 (m-40) cc_final: 0.6735 (p0) REVERT: B 233 LYS cc_start: 0.7660 (tptm) cc_final: 0.7241 (tptm) REVERT: B 252 LYS cc_start: 0.8369 (ptpp) cc_final: 0.8076 (tppt) REVERT: C 135 CYS cc_start: 0.8043 (m) cc_final: 0.7809 (m) REVERT: C 145 MET cc_start: 0.6948 (mpp) cc_final: 0.6722 (mpp) REVERT: C 173 ASP cc_start: 0.8317 (t0) cc_final: 0.8066 (t0) REVERT: C 232 ASN cc_start: 0.7480 (m-40) cc_final: 0.6768 (p0) REVERT: C 233 LYS cc_start: 0.8189 (tppp) cc_final: 0.7835 (tppp) REVERT: C 271 ASN cc_start: 0.8719 (t0) cc_final: 0.8285 (t0) REVERT: C 279 MET cc_start: 0.8537 (mtm) cc_final: 0.8187 (mmp) REVERT: D 76 THR cc_start: 0.8605 (p) cc_final: 0.8319 (p) REVERT: D 80 LYS cc_start: 0.8923 (mttt) cc_final: 0.8697 (mttp) REVERT: D 145 MET cc_start: 0.7269 (mpp) cc_final: 0.6850 (mpp) REVERT: D 160 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8148 (ttm170) REVERT: D 232 ASN cc_start: 0.7178 (m-40) cc_final: 0.6622 (p0) REVERT: D 233 LYS cc_start: 0.8149 (tppp) cc_final: 0.7604 (mmmm) REVERT: D 252 LYS cc_start: 0.8515 (ptpp) cc_final: 0.7776 (tppt) REVERT: D 258 GLN cc_start: 0.9157 (tp40) cc_final: 0.8689 (tp40) REVERT: D 271 ASN cc_start: 0.8700 (t0) cc_final: 0.8140 (t0) REVERT: E 143 LEU cc_start: 0.9360 (mt) cc_final: 0.8980 (mt) REVERT: E 145 MET cc_start: 0.7170 (mpp) cc_final: 0.6889 (mpp) REVERT: E 169 LEU cc_start: 0.8728 (tp) cc_final: 0.8393 (tp) REVERT: E 240 LYS cc_start: 0.8732 (mttm) cc_final: 0.8430 (mttm) REVERT: E 252 LYS cc_start: 0.8458 (ptpp) cc_final: 0.7944 (tppt) REVERT: E 258 GLN cc_start: 0.9134 (tp40) cc_final: 0.8680 (tp-100) REVERT: E 271 ASN cc_start: 0.8803 (t0) cc_final: 0.8450 (t0) REVERT: F 76 THR cc_start: 0.8857 (p) cc_final: 0.8464 (p) REVERT: F 80 LYS cc_start: 0.9164 (mttt) cc_final: 0.8931 (mttp) REVERT: F 81 GLN cc_start: 0.8854 (tm130) cc_final: 0.8380 (pt0) REVERT: F 101 ASN cc_start: 0.7367 (m110) cc_final: 0.7096 (m110) REVERT: F 173 ASP cc_start: 0.8505 (t0) cc_final: 0.8128 (m-30) REVERT: F 182 VAL cc_start: 0.8062 (t) cc_final: 0.7762 (t) REVERT: F 209 MET cc_start: 0.2549 (mtt) cc_final: 0.1479 (mtp) REVERT: F 258 GLN cc_start: 0.9158 (tp40) cc_final: 0.8652 (tp-100) REVERT: F 271 ASN cc_start: 0.8738 (t0) cc_final: 0.8462 (t0) REVERT: F 292 TYR cc_start: 0.8494 (m-10) cc_final: 0.8247 (m-80) REVERT: G 73 PHE cc_start: 0.7611 (t80) cc_final: 0.6483 (t80) REVERT: G 86 MET cc_start: 0.7557 (tpp) cc_final: 0.6754 (ttm) REVERT: G 108 GLU cc_start: 0.7608 (tp30) cc_final: 0.7101 (tp30) REVERT: G 122 MET cc_start: 0.8479 (ttt) cc_final: 0.7990 (tmm) REVERT: G 123 ILE cc_start: 0.9308 (pt) cc_final: 0.8942 (pt) REVERT: G 143 LEU cc_start: 0.9412 (mt) cc_final: 0.9069 (mt) REVERT: G 146 ASN cc_start: 0.8683 (m-40) cc_final: 0.8478 (m110) REVERT: G 169 LEU cc_start: 0.8828 (tp) cc_final: 0.8449 (tp) REVERT: G 174 GLU cc_start: 0.7778 (mp0) cc_final: 0.7557 (mp0) REVERT: G 251 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7152 (tm-30) REVERT: G 258 GLN cc_start: 0.9168 (tp40) cc_final: 0.8835 (mm-40) REVERT: G 267 LEU cc_start: 0.8190 (mt) cc_final: 0.7961 (mm) REVERT: G 271 ASN cc_start: 0.9253 (t0) cc_final: 0.8855 (p0) REVERT: H 80 LYS cc_start: 0.9069 (mttt) cc_final: 0.8763 (mttp) REVERT: H 145 MET cc_start: 0.7100 (mpp) cc_final: 0.6578 (mpp) REVERT: H 209 MET cc_start: 0.1851 (mtt) cc_final: 0.1330 (mtp) REVERT: H 232 ASN cc_start: 0.7202 (m-40) cc_final: 0.6744 (p0) REVERT: H 233 LYS cc_start: 0.8218 (tppp) cc_final: 0.7742 (mmmm) REVERT: H 251 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7497 (tm-30) REVERT: H 252 LYS cc_start: 0.8667 (ptpp) cc_final: 0.7878 (tppt) REVERT: H 258 GLN cc_start: 0.9113 (tp40) cc_final: 0.8658 (tp40) REVERT: H 271 ASN cc_start: 0.8815 (t0) cc_final: 0.8437 (t0) REVERT: I 73 PHE cc_start: 0.7693 (t80) cc_final: 0.6206 (t80) REVERT: I 86 MET cc_start: 0.7316 (tpp) cc_final: 0.6749 (ttm) REVERT: I 108 GLU cc_start: 0.7570 (tp30) cc_final: 0.7270 (tp30) REVERT: I 145 MET cc_start: 0.7242 (mpp) cc_final: 0.6946 (mpp) REVERT: I 169 LEU cc_start: 0.8656 (tp) cc_final: 0.8445 (tp) REVERT: I 232 ASN cc_start: 0.7333 (m-40) cc_final: 0.6818 (p0) REVERT: I 233 LYS cc_start: 0.8181 (tppp) cc_final: 0.7614 (mmmm) REVERT: I 251 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7216 (tm-30) REVERT: I 258 GLN cc_start: 0.9027 (tp40) cc_final: 0.8665 (tp40) REVERT: J 73 PHE cc_start: 0.7612 (t80) cc_final: 0.6415 (t80) REVERT: J 80 LYS cc_start: 0.9024 (mttt) cc_final: 0.8716 (mttp) REVERT: J 86 MET cc_start: 0.7449 (tpp) cc_final: 0.6759 (ttm) REVERT: J 108 GLU cc_start: 0.7484 (tp30) cc_final: 0.7019 (tp30) REVERT: J 112 GLU cc_start: 0.7388 (tp30) cc_final: 0.7175 (tp30) REVERT: J 142 GLU cc_start: 0.7999 (tp30) cc_final: 0.7693 (tp30) REVERT: J 145 MET cc_start: 0.7207 (mpp) cc_final: 0.6816 (mpp) REVERT: J 173 ASP cc_start: 0.8421 (t0) cc_final: 0.8054 (t0) REVERT: J 220 ARG cc_start: 0.8181 (ptp-170) cc_final: 0.7947 (mtp180) REVERT: J 232 ASN cc_start: 0.7304 (m-40) cc_final: 0.7033 (p0) REVERT: J 233 LYS cc_start: 0.8234 (tppp) cc_final: 0.7593 (mmmm) REVERT: J 289 ASN cc_start: 0.8554 (p0) cc_final: 0.7966 (p0) REVERT: K 73 PHE cc_start: 0.7699 (t80) cc_final: 0.6371 (t80) REVERT: K 108 GLU cc_start: 0.7550 (tp30) cc_final: 0.6952 (tp30) REVERT: K 145 MET cc_start: 0.7053 (mpp) cc_final: 0.6640 (mpp) REVERT: K 232 ASN cc_start: 0.7307 (m-40) cc_final: 0.6856 (p0) REVERT: K 233 LYS cc_start: 0.8369 (tppp) cc_final: 0.7860 (mmmm) REVERT: K 251 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7420 (tm-30) REVERT: K 258 GLN cc_start: 0.9090 (tp40) cc_final: 0.8660 (tp40) REVERT: K 271 ASN cc_start: 0.8976 (t0) cc_final: 0.8575 (t0) REVERT: L 86 MET cc_start: 0.7459 (tpp) cc_final: 0.6453 (ttm) REVERT: L 112 GLU cc_start: 0.7308 (tp30) cc_final: 0.6849 (tp30) REVERT: L 145 MET cc_start: 0.7227 (mpp) cc_final: 0.6873 (mpp) REVERT: L 251 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7495 (tm-30) REVERT: L 252 LYS cc_start: 0.8554 (ptpp) cc_final: 0.7565 (tppt) REVERT: L 258 GLN cc_start: 0.8986 (tp40) cc_final: 0.8729 (tp40) REVERT: L 260 ILE cc_start: 0.9193 (mt) cc_final: 0.8965 (mt) REVERT: L 270 LEU cc_start: 0.9320 (tt) cc_final: 0.8809 (pp) REVERT: M 86 MET cc_start: 0.7471 (tpp) cc_final: 0.6833 (ttm) REVERT: M 145 MET cc_start: 0.7043 (mpp) cc_final: 0.6540 (mpp) REVERT: M 162 ARG cc_start: 0.7721 (ttt-90) cc_final: 0.7496 (ttt-90) REVERT: M 232 ASN cc_start: 0.7183 (m-40) cc_final: 0.6758 (p0) REVERT: M 233 LYS cc_start: 0.8227 (tppp) cc_final: 0.7634 (mmmm) REVERT: M 251 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7643 (tm-30) REVERT: M 258 GLN cc_start: 0.9099 (tp40) cc_final: 0.8571 (tp40) REVERT: M 267 LEU cc_start: 0.8557 (mm) cc_final: 0.8214 (mm) REVERT: N 80 LYS cc_start: 0.9069 (mttt) cc_final: 0.8728 (mttp) REVERT: N 81 GLN cc_start: 0.8779 (tm130) cc_final: 0.8285 (pt0) REVERT: N 86 MET cc_start: 0.7963 (ttm) cc_final: 0.7218 (ttm) REVERT: N 112 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7623 (mt-10) REVERT: N 169 LEU cc_start: 0.8648 (tp) cc_final: 0.8342 (tp) REVERT: N 209 MET cc_start: 0.2245 (mtt) cc_final: 0.1537 (mtp) REVERT: N 232 ASN cc_start: 0.7089 (m-40) cc_final: 0.6468 (p0) REVERT: N 240 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8330 (ttpt) REVERT: N 251 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7746 (tm-30) REVERT: O 80 LYS cc_start: 0.8961 (mttt) cc_final: 0.8741 (mttp) REVERT: O 86 MET cc_start: 0.7405 (tpp) cc_final: 0.6543 (ttm) REVERT: O 112 GLU cc_start: 0.8436 (pt0) cc_final: 0.8099 (pt0) REVERT: O 145 MET cc_start: 0.7297 (mpp) cc_final: 0.6733 (mpp) REVERT: O 155 LEU cc_start: 0.8772 (tp) cc_final: 0.8522 (tp) REVERT: O 181 GLU cc_start: 0.9066 (tt0) cc_final: 0.8380 (pm20) REVERT: O 182 VAL cc_start: 0.8533 (t) cc_final: 0.7585 (t) REVERT: O 200 MET cc_start: 0.6930 (tpp) cc_final: 0.6400 (mmm) REVERT: O 235 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8653 (mmtt) REVERT: O 251 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7193 (tm-30) REVERT: O 258 GLN cc_start: 0.9096 (tp40) cc_final: 0.8663 (tp40) REVERT: P 80 LYS cc_start: 0.9094 (mttt) cc_final: 0.8815 (mttp) REVERT: P 86 MET cc_start: 0.7432 (ttm) cc_final: 0.6965 (ttm) REVERT: P 143 LEU cc_start: 0.9270 (mt) cc_final: 0.8842 (mt) REVERT: P 145 MET cc_start: 0.6934 (mpp) cc_final: 0.5929 (mpp) REVERT: P 232 ASN cc_start: 0.7084 (m-40) cc_final: 0.6667 (p0) REVERT: P 233 LYS cc_start: 0.8267 (tppp) cc_final: 0.7563 (mmmm) REVERT: P 235 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8913 (mmtt) REVERT: P 251 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7324 (tm-30) REVERT: P 252 LYS cc_start: 0.8662 (ptpp) cc_final: 0.7740 (tppt) REVERT: P 258 GLN cc_start: 0.9046 (tp40) cc_final: 0.8563 (tp40) REVERT: Q 143 LEU cc_start: 0.9352 (mt) cc_final: 0.8995 (mt) REVERT: Q 145 MET cc_start: 0.7121 (mpp) cc_final: 0.6626 (mpp) REVERT: Q 232 ASN cc_start: 0.7150 (m-40) cc_final: 0.6734 (p0) REVERT: Q 233 LYS cc_start: 0.8199 (tppp) cc_final: 0.7382 (mmmm) REVERT: Q 240 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8543 (tttt) REVERT: Q 251 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7172 (tm-30) REVERT: Q 252 LYS cc_start: 0.8474 (ptpp) cc_final: 0.7559 (tppt) REVERT: Q 258 GLN cc_start: 0.9111 (tp40) cc_final: 0.8656 (tp40) REVERT: Q 271 ASN cc_start: 0.8790 (t0) cc_final: 0.8479 (t0) REVERT: R 86 MET cc_start: 0.7587 (tpp) cc_final: 0.6685 (ttm) REVERT: R 101 ASN cc_start: 0.7166 (m110) cc_final: 0.6961 (m-40) REVERT: R 232 ASN cc_start: 0.7215 (m-40) cc_final: 0.6699 (p0) REVERT: R 251 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7518 (tm-30) REVERT: R 252 LYS cc_start: 0.8567 (ptpp) cc_final: 0.7957 (tppt) REVERT: R 258 GLN cc_start: 0.9078 (tp40) cc_final: 0.8546 (tp40) REVERT: R 259 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8825 (pt0) outliers start: 6 outliers final: 1 residues processed: 1331 average time/residue: 0.2228 time to fit residues: 460.3991 Evaluate side-chains 1114 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1113 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 413 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 117 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN B 81 GLN B 117 ASN B 167 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 117 ASN C 146 ASN C 262 GLN D 81 GLN D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 117 ASN F 81 GLN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 117 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN I 81 GLN I 117 ASN J 81 GLN J 117 ASN ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN K 117 ASN K 119 ASN K 146 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN M 146 ASN ** M 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN O 81 GLN O 146 ASN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 272 HIS P 81 GLN P 117 ASN ** P 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 GLN R 146 ASN ** R 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.167854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131761 restraints weight = 65826.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.136775 restraints weight = 43115.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140367 restraints weight = 31327.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142976 restraints weight = 24566.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.144859 restraints weight = 20390.131| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34326 Z= 0.203 Angle : 0.804 12.204 46422 Z= 0.381 Chirality : 0.045 0.259 5346 Planarity : 0.005 0.068 5940 Dihedral : 11.907 172.762 4842 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4158 helix: 0.05 (0.10), residues: 2484 sheet: -1.32 (0.20), residues: 630 loop : -0.02 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 220 TYR 0.023 0.001 TYR J 292 PHE 0.017 0.002 PHE F 141 TRP 0.018 0.001 TRP P 121 HIS 0.008 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00426 (34326) covalent geometry : angle 0.80351 (46422) hydrogen bonds : bond 0.03616 ( 1852) hydrogen bonds : angle 4.71345 ( 5448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1277 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8973 (mttt) cc_final: 0.8707 (mttp) REVERT: A 112 GLU cc_start: 0.8802 (pm20) cc_final: 0.8247 (pm20) REVERT: A 169 LEU cc_start: 0.8487 (tp) cc_final: 0.7885 (tp) REVERT: A 174 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 232 ASN cc_start: 0.7376 (m-40) cc_final: 0.6463 (p0) REVERT: A 233 LYS cc_start: 0.8216 (tppp) cc_final: 0.7776 (tppp) REVERT: A 251 GLU cc_start: 0.8732 (mm-30) cc_final: 0.7517 (tm-30) REVERT: A 252 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8184 (ptpp) REVERT: A 258 GLN cc_start: 0.9093 (tp40) cc_final: 0.8581 (tp40) REVERT: B 80 LYS cc_start: 0.9064 (mttt) cc_final: 0.8824 (mmtm) REVERT: B 101 ASN cc_start: 0.7471 (m110) cc_final: 0.7254 (m110) REVERT: B 143 LEU cc_start: 0.9324 (mt) cc_final: 0.8951 (mt) REVERT: B 145 MET cc_start: 0.7269 (mpp) cc_final: 0.6884 (mpp) REVERT: B 184 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 190 GLN cc_start: 0.8563 (pt0) cc_final: 0.8081 (pt0) REVERT: B 209 MET cc_start: -0.0113 (ttt) cc_final: -0.0745 (mmm) REVERT: B 232 ASN cc_start: 0.7335 (m-40) cc_final: 0.6365 (p0) REVERT: B 233 LYS cc_start: 0.7710 (tptm) cc_final: 0.7381 (mmmm) REVERT: B 252 LYS cc_start: 0.8447 (ptpp) cc_final: 0.8105 (tppt) REVERT: C 145 MET cc_start: 0.7235 (mpp) cc_final: 0.6737 (mpp) REVERT: C 169 LEU cc_start: 0.8737 (tp) cc_final: 0.8508 (tp) REVERT: C 182 VAL cc_start: 0.8296 (t) cc_final: 0.8036 (t) REVERT: C 187 ARG cc_start: 0.8744 (ptt90) cc_final: 0.8513 (ppt170) REVERT: C 224 ARG cc_start: 0.6977 (mtt180) cc_final: 0.6267 (mtt180) REVERT: C 232 ASN cc_start: 0.7533 (m-40) cc_final: 0.6630 (p0) REVERT: C 233 LYS cc_start: 0.8166 (tppp) cc_final: 0.7845 (tppp) REVERT: C 258 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8861 (tp40) REVERT: C 260 ILE cc_start: 0.9086 (mt) cc_final: 0.8768 (mt) REVERT: C 271 ASN cc_start: 0.8621 (t0) cc_final: 0.8052 (t0) REVERT: C 279 MET cc_start: 0.8545 (mtm) cc_final: 0.8152 (mmp) REVERT: D 76 THR cc_start: 0.8653 (p) cc_final: 0.8312 (p) REVERT: D 80 LYS cc_start: 0.8903 (mttt) cc_final: 0.8674 (mttp) REVERT: D 145 MET cc_start: 0.7341 (mpp) cc_final: 0.6956 (mpp) REVERT: D 232 ASN cc_start: 0.7282 (m-40) cc_final: 0.6424 (p0) REVERT: D 235 LYS cc_start: 0.9179 (mttt) cc_final: 0.8814 (mmmt) REVERT: D 258 GLN cc_start: 0.9145 (tp40) cc_final: 0.8736 (tp40) REVERT: D 271 ASN cc_start: 0.8669 (t0) cc_final: 0.8002 (t0) REVERT: E 143 LEU cc_start: 0.9252 (mt) cc_final: 0.8888 (mt) REVERT: E 145 MET cc_start: 0.7033 (mpp) cc_final: 0.6274 (mpp) REVERT: E 169 LEU cc_start: 0.8870 (tp) cc_final: 0.8408 (tp) REVERT: E 182 VAL cc_start: 0.8111 (t) cc_final: 0.7827 (t) REVERT: E 232 ASN cc_start: 0.7340 (m-40) cc_final: 0.6247 (p0) REVERT: E 233 LYS cc_start: 0.7636 (tptm) cc_final: 0.7183 (tptm) REVERT: E 240 LYS cc_start: 0.8715 (mttm) cc_final: 0.8323 (tttt) REVERT: E 252 LYS cc_start: 0.8440 (ptpp) cc_final: 0.7919 (tppt) REVERT: E 258 GLN cc_start: 0.9136 (tp40) cc_final: 0.8666 (tp-100) REVERT: F 101 ASN cc_start: 0.7316 (m110) cc_final: 0.7054 (m110) REVERT: F 169 LEU cc_start: 0.8674 (tp) cc_final: 0.8317 (tp) REVERT: F 182 VAL cc_start: 0.8111 (t) cc_final: 0.7902 (t) REVERT: F 184 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8275 (mt-10) REVERT: F 190 GLN cc_start: 0.8484 (pt0) cc_final: 0.8255 (pt0) REVERT: F 209 MET cc_start: 0.2652 (mtt) cc_final: 0.0923 (mtp) REVERT: F 232 ASN cc_start: 0.7365 (m-40) cc_final: 0.6166 (p0) REVERT: F 258 GLN cc_start: 0.9109 (tp40) cc_final: 0.8678 (tp-100) REVERT: G 73 PHE cc_start: 0.7716 (t80) cc_final: 0.6783 (t80) REVERT: G 80 LYS cc_start: 0.8993 (mttt) cc_final: 0.8657 (mttp) REVERT: G 86 MET cc_start: 0.7638 (tpp) cc_final: 0.6530 (ttm) REVERT: G 108 GLU cc_start: 0.7603 (tp30) cc_final: 0.7210 (tp30) REVERT: G 122 MET cc_start: 0.8796 (ttt) cc_final: 0.8361 (tmm) REVERT: G 143 LEU cc_start: 0.9228 (mt) cc_final: 0.8986 (mt) REVERT: G 145 MET cc_start: 0.7031 (mpp) cc_final: 0.6617 (mpp) REVERT: G 190 GLN cc_start: 0.7926 (pp30) cc_final: 0.7586 (pp30) REVERT: G 232 ASN cc_start: 0.7413 (m-40) cc_final: 0.6886 (p0) REVERT: G 233 LYS cc_start: 0.8363 (tppp) cc_final: 0.7734 (mmmm) REVERT: G 251 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7114 (tm-30) REVERT: G 258 GLN cc_start: 0.9112 (tp40) cc_final: 0.8682 (tp40) REVERT: G 267 LEU cc_start: 0.8325 (mt) cc_final: 0.7850 (mm) REVERT: G 271 ASN cc_start: 0.9306 (t0) cc_final: 0.9043 (p0) REVERT: H 145 MET cc_start: 0.7291 (mpp) cc_final: 0.6953 (mpp) REVERT: H 169 LEU cc_start: 0.8793 (tp) cc_final: 0.8414 (tp) REVERT: H 209 MET cc_start: 0.2154 (mtt) cc_final: 0.1356 (mtp) REVERT: H 232 ASN cc_start: 0.7216 (m-40) cc_final: 0.6461 (p0) REVERT: H 233 LYS cc_start: 0.8193 (tppp) cc_final: 0.7754 (mmmm) REVERT: H 236 LYS cc_start: 0.8616 (tptp) cc_final: 0.8316 (tppt) REVERT: H 251 GLU cc_start: 0.8755 (mm-30) cc_final: 0.7469 (tm-30) REVERT: H 252 LYS cc_start: 0.8670 (ptpp) cc_final: 0.7884 (tppt) REVERT: H 271 ASN cc_start: 0.8739 (t0) cc_final: 0.8378 (t0) REVERT: I 73 PHE cc_start: 0.7730 (t80) cc_final: 0.6385 (t80) REVERT: I 80 LYS cc_start: 0.9006 (mttt) cc_final: 0.8730 (mttp) REVERT: I 108 GLU cc_start: 0.7496 (tp30) cc_final: 0.6984 (tp30) REVERT: I 209 MET cc_start: 0.0533 (mtp) cc_final: 0.0235 (ttt) REVERT: I 232 ASN cc_start: 0.7172 (m-40) cc_final: 0.6550 (p0) REVERT: I 233 LYS cc_start: 0.8394 (tppp) cc_final: 0.7801 (mmmm) REVERT: I 251 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7208 (tm-30) REVERT: I 258 GLN cc_start: 0.8982 (tp40) cc_final: 0.8771 (mm-40) REVERT: J 73 PHE cc_start: 0.7756 (t80) cc_final: 0.6680 (t80) REVERT: J 80 LYS cc_start: 0.9048 (mttt) cc_final: 0.8772 (mttp) REVERT: J 108 GLU cc_start: 0.7579 (tp30) cc_final: 0.7192 (tp30) REVERT: J 112 GLU cc_start: 0.7423 (tp30) cc_final: 0.7214 (tp30) REVERT: J 220 ARG cc_start: 0.8255 (ptp-170) cc_final: 0.7994 (mtp85) REVERT: J 232 ASN cc_start: 0.7342 (m-40) cc_final: 0.6897 (p0) REVERT: J 233 LYS cc_start: 0.8402 (tppp) cc_final: 0.7791 (mmmm) REVERT: J 251 GLU cc_start: 0.8533 (mm-30) cc_final: 0.6904 (tm-30) REVERT: J 258 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8512 (tp40) REVERT: J 292 TYR cc_start: 0.8514 (m-10) cc_final: 0.8292 (m-10) REVERT: K 73 PHE cc_start: 0.7796 (t80) cc_final: 0.6600 (t80) REVERT: K 80 LYS cc_start: 0.8881 (mttt) cc_final: 0.8597 (mttp) REVERT: K 108 GLU cc_start: 0.7499 (tp30) cc_final: 0.7016 (tp30) REVERT: K 145 MET cc_start: 0.7330 (mpp) cc_final: 0.7019 (mpp) REVERT: K 209 MET cc_start: 0.0140 (ttt) cc_final: -0.0768 (mmm) REVERT: K 232 ASN cc_start: 0.7385 (m-40) cc_final: 0.6869 (p0) REVERT: K 233 LYS cc_start: 0.8207 (tppp) cc_final: 0.7817 (mmmm) REVERT: K 236 LYS cc_start: 0.8627 (tptp) cc_final: 0.8359 (tppt) REVERT: K 251 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7379 (tm-30) REVERT: L 86 MET cc_start: 0.6738 (tpp) cc_final: 0.6511 (ttm) REVERT: L 112 GLU cc_start: 0.7241 (tp30) cc_final: 0.6996 (tp30) REVERT: L 232 ASN cc_start: 0.7259 (m-40) cc_final: 0.6536 (p0) REVERT: L 251 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7521 (tm-30) REVERT: L 260 ILE cc_start: 0.9067 (mt) cc_final: 0.8743 (mt) REVERT: L 292 TYR cc_start: 0.8472 (m-80) cc_final: 0.8111 (m-80) REVERT: M 80 LYS cc_start: 0.9018 (mttt) cc_final: 0.8752 (mttp) REVERT: M 86 MET cc_start: 0.7648 (tpp) cc_final: 0.6921 (ttm) REVERT: M 114 ARG cc_start: 0.9073 (ttp-170) cc_final: 0.8550 (ttp80) REVERT: M 122 MET cc_start: 0.7561 (tmm) cc_final: 0.7308 (tmm) REVERT: M 135 CYS cc_start: 0.8206 (m) cc_final: 0.8002 (m) REVERT: M 145 MET cc_start: 0.7379 (mpp) cc_final: 0.6526 (mpp) REVERT: M 169 LEU cc_start: 0.8783 (tp) cc_final: 0.8568 (tp) REVERT: M 200 MET cc_start: 0.7301 (tpp) cc_final: 0.7069 (tpp) REVERT: M 232 ASN cc_start: 0.7284 (m-40) cc_final: 0.6427 (p0) REVERT: M 233 LYS cc_start: 0.8107 (tppp) cc_final: 0.7400 (mmmm) REVERT: M 251 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7615 (tm-30) REVERT: M 252 LYS cc_start: 0.8499 (ptpp) cc_final: 0.7902 (tppt) REVERT: M 258 GLN cc_start: 0.9014 (tp40) cc_final: 0.8628 (tp40) REVERT: N 77 GLN cc_start: 0.8896 (pp30) cc_final: 0.8478 (pp30) REVERT: N 80 LYS cc_start: 0.9006 (mttt) cc_final: 0.8692 (mttp) REVERT: N 112 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7573 (mt-10) REVERT: N 169 LEU cc_start: 0.8670 (tp) cc_final: 0.7966 (tp) REVERT: N 209 MET cc_start: 0.2507 (mtt) cc_final: 0.1525 (mtp) REVERT: N 232 ASN cc_start: 0.7168 (m-40) cc_final: 0.6440 (p0) REVERT: N 251 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7572 (tm-30) REVERT: N 258 GLN cc_start: 0.8918 (tp40) cc_final: 0.8644 (tp-100) REVERT: O 86 MET cc_start: 0.7525 (tpp) cc_final: 0.6458 (ttm) REVERT: O 145 MET cc_start: 0.7409 (mpp) cc_final: 0.6948 (mpp) REVERT: O 155 LEU cc_start: 0.8909 (tp) cc_final: 0.8706 (tp) REVERT: O 169 LEU cc_start: 0.8632 (tp) cc_final: 0.7940 (tp) REVERT: O 235 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8687 (mmtt) REVERT: O 258 GLN cc_start: 0.9034 (tp40) cc_final: 0.8643 (tp40) REVERT: P 86 MET cc_start: 0.7762 (ttm) cc_final: 0.7090 (ttm) REVERT: P 143 LEU cc_start: 0.9247 (mt) cc_final: 0.8783 (mt) REVERT: P 145 MET cc_start: 0.7339 (mpp) cc_final: 0.6519 (mpp) REVERT: P 174 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8060 (mm-30) REVERT: P 232 ASN cc_start: 0.7062 (m-40) cc_final: 0.6488 (p0) REVERT: P 233 LYS cc_start: 0.8235 (tppp) cc_final: 0.7559 (mmmm) REVERT: P 251 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7407 (tm-30) REVERT: P 252 LYS cc_start: 0.8525 (ptpp) cc_final: 0.7897 (tppt) REVERT: P 258 GLN cc_start: 0.9040 (tp40) cc_final: 0.8537 (tp40) REVERT: Q 143 LEU cc_start: 0.9393 (mt) cc_final: 0.9098 (mt) REVERT: Q 145 MET cc_start: 0.7238 (mpp) cc_final: 0.6700 (mpp) REVERT: Q 169 LEU cc_start: 0.8593 (tp) cc_final: 0.8169 (tp) REVERT: Q 236 LYS cc_start: 0.8683 (tptp) cc_final: 0.8418 (tppt) REVERT: Q 240 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8441 (tttt) REVERT: Q 251 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7251 (tm-30) REVERT: Q 271 ASN cc_start: 0.8702 (t0) cc_final: 0.8420 (t0) REVERT: Q 289 ASN cc_start: 0.8658 (p0) cc_final: 0.7874 (p0) REVERT: R 86 MET cc_start: 0.6877 (tpp) cc_final: 0.6639 (ttm) REVERT: R 169 LEU cc_start: 0.8496 (tp) cc_final: 0.8066 (tp) REVERT: R 232 ASN cc_start: 0.7213 (m-40) cc_final: 0.6550 (p0) REVERT: R 236 LYS cc_start: 0.8642 (tptp) cc_final: 0.8393 (tppt) REVERT: R 251 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7465 (tm-30) REVERT: R 252 LYS cc_start: 0.8523 (ptpp) cc_final: 0.8310 (ptpp) REVERT: R 289 ASN cc_start: 0.8958 (p0) cc_final: 0.8591 (p0) REVERT: R 292 TYR cc_start: 0.8780 (m-10) cc_final: 0.8391 (m-10) outliers start: 0 outliers final: 0 residues processed: 1277 average time/residue: 0.2279 time to fit residues: 453.0402 Evaluate side-chains 1077 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1077 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 173 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 0.0980 chunk 246 optimal weight: 10.0000 chunk 409 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 249 optimal weight: 20.0000 chunk 301 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN B 146 ASN B 167 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 146 ASN D 81 GLN D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN G 146 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN H 146 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 146 ASN K 81 GLN K 146 ASN K 271 ASN M 81 GLN N 81 GLN N 117 ASN O 81 GLN O 146 ASN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN P 271 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** Q 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 GLN R 146 ASN ** R 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.166176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129831 restraints weight = 66732.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134433 restraints weight = 45089.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.137772 restraints weight = 33622.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140211 restraints weight = 26929.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.142069 restraints weight = 22717.384| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34326 Z= 0.226 Angle : 0.838 13.924 46422 Z= 0.399 Chirality : 0.046 0.286 5346 Planarity : 0.006 0.179 5940 Dihedral : 11.665 173.332 4842 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4158 helix: -0.10 (0.09), residues: 2574 sheet: -1.33 (0.21), residues: 630 loop : -0.24 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 194 TYR 0.020 0.001 TYR Q 113 PHE 0.018 0.002 PHE F 297 TRP 0.029 0.002 TRP A 246 HIS 0.006 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00478 (34326) covalent geometry : angle 0.83816 (46422) hydrogen bonds : bond 0.03725 ( 1852) hydrogen bonds : angle 4.88924 ( 5448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1257 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8986 (mttt) cc_final: 0.8715 (mttp) REVERT: A 169 LEU cc_start: 0.8631 (tp) cc_final: 0.7975 (tp) REVERT: A 173 ASP cc_start: 0.8527 (t0) cc_final: 0.8183 (t0) REVERT: A 209 MET cc_start: -0.0279 (mtp) cc_final: -0.0810 (mmm) REVERT: A 232 ASN cc_start: 0.7670 (m-40) cc_final: 0.6507 (p0) REVERT: A 233 LYS cc_start: 0.8273 (tppp) cc_final: 0.7973 (tppp) REVERT: A 251 GLU cc_start: 0.8750 (mm-30) cc_final: 0.7526 (tm-30) REVERT: A 252 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8106 (ptpp) REVERT: A 258 GLN cc_start: 0.9133 (tp40) cc_final: 0.8605 (tp40) REVERT: A 279 MET cc_start: 0.8534 (mtt) cc_final: 0.8246 (mtm) REVERT: B 80 LYS cc_start: 0.9011 (mttt) cc_final: 0.8751 (mmtm) REVERT: B 101 ASN cc_start: 0.7562 (m110) cc_final: 0.7342 (m110) REVERT: B 143 LEU cc_start: 0.9302 (mt) cc_final: 0.8892 (mt) REVERT: B 145 MET cc_start: 0.7159 (mpp) cc_final: 0.6400 (mpp) REVERT: B 184 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 190 GLN cc_start: 0.8482 (pt0) cc_final: 0.8144 (pt0) REVERT: B 209 MET cc_start: 0.0563 (ttt) cc_final: 0.0018 (tpt) REVERT: B 232 ASN cc_start: 0.7332 (m-40) cc_final: 0.6231 (p0) REVERT: B 252 LYS cc_start: 0.8423 (ptpp) cc_final: 0.8108 (tppt) REVERT: B 260 ILE cc_start: 0.9040 (mt) cc_final: 0.8764 (mt) REVERT: C 112 GLU cc_start: 0.8711 (pt0) cc_final: 0.8497 (pt0) REVERT: C 182 VAL cc_start: 0.8247 (t) cc_final: 0.8022 (t) REVERT: C 184 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8250 (mt-10) REVERT: C 187 ARG cc_start: 0.8741 (ptt90) cc_final: 0.8455 (ppt170) REVERT: C 205 VAL cc_start: 0.6325 (t) cc_final: 0.5992 (t) REVERT: C 232 ASN cc_start: 0.7609 (m-40) cc_final: 0.6534 (p0) REVERT: C 233 LYS cc_start: 0.8164 (tppp) cc_final: 0.7573 (mmmm) REVERT: C 260 ILE cc_start: 0.9072 (mt) cc_final: 0.8780 (mt) REVERT: C 279 MET cc_start: 0.8577 (mtm) cc_final: 0.8224 (mmp) REVERT: D 77 GLN cc_start: 0.8834 (pp30) cc_final: 0.8598 (pp30) REVERT: D 112 GLU cc_start: 0.9042 (pm20) cc_final: 0.8785 (pm20) REVERT: D 145 MET cc_start: 0.7396 (mpp) cc_final: 0.7181 (mpp) REVERT: D 209 MET cc_start: -0.0135 (ttt) cc_final: -0.1052 (mmm) REVERT: D 232 ASN cc_start: 0.7628 (m-40) cc_final: 0.6473 (p0) REVERT: D 235 LYS cc_start: 0.9126 (mttt) cc_final: 0.8776 (mmmt) REVERT: D 258 GLN cc_start: 0.9038 (tp40) cc_final: 0.8633 (tp40) REVERT: D 271 ASN cc_start: 0.8595 (t0) cc_final: 0.7941 (t0) REVERT: E 80 LYS cc_start: 0.9102 (mttt) cc_final: 0.8822 (mttm) REVERT: E 143 LEU cc_start: 0.9263 (mt) cc_final: 0.8670 (mt) REVERT: E 145 MET cc_start: 0.7278 (mpp) cc_final: 0.6629 (mpp) REVERT: E 232 ASN cc_start: 0.7420 (m-40) cc_final: 0.6178 (p0) REVERT: E 233 LYS cc_start: 0.8151 (tppp) cc_final: 0.7465 (mmmm) REVERT: E 240 LYS cc_start: 0.8734 (mttm) cc_final: 0.8277 (ttpt) REVERT: E 252 LYS cc_start: 0.8421 (ptpp) cc_final: 0.7891 (tppt) REVERT: E 258 GLN cc_start: 0.9034 (tp40) cc_final: 0.8578 (tp-100) REVERT: E 289 ASN cc_start: 0.8405 (p0) cc_final: 0.7760 (p0) REVERT: E 292 TYR cc_start: 0.8437 (m-10) cc_final: 0.8167 (m-80) REVERT: F 73 PHE cc_start: 0.6403 (t80) cc_final: 0.5867 (t80) REVERT: F 80 LYS cc_start: 0.9094 (mttt) cc_final: 0.8893 (mmtm) REVERT: F 101 ASN cc_start: 0.7272 (m110) cc_final: 0.7039 (m110) REVERT: F 182 VAL cc_start: 0.8136 (t) cc_final: 0.7929 (t) REVERT: F 184 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8305 (mt-10) REVERT: F 190 GLN cc_start: 0.8556 (pt0) cc_final: 0.8277 (pt0) REVERT: F 205 VAL cc_start: 0.6435 (t) cc_final: 0.5793 (t) REVERT: F 209 MET cc_start: 0.2882 (mtt) cc_final: 0.0988 (ttm) REVERT: F 232 ASN cc_start: 0.7504 (m-40) cc_final: 0.5862 (p0) REVERT: F 235 LYS cc_start: 0.9152 (mttt) cc_final: 0.8676 (mmmt) REVERT: F 258 GLN cc_start: 0.9130 (tp40) cc_final: 0.8813 (tp-100) REVERT: F 279 MET cc_start: 0.8383 (mtm) cc_final: 0.7777 (mmp) REVERT: G 73 PHE cc_start: 0.7690 (t80) cc_final: 0.6728 (t80) REVERT: G 86 MET cc_start: 0.7806 (tpp) cc_final: 0.6601 (ttm) REVERT: G 108 GLU cc_start: 0.7477 (tp30) cc_final: 0.7095 (tp30) REVERT: G 143 LEU cc_start: 0.9239 (mt) cc_final: 0.8856 (mt) REVERT: G 145 MET cc_start: 0.7304 (mpp) cc_final: 0.6834 (mpp) REVERT: G 232 ASN cc_start: 0.7433 (m-40) cc_final: 0.6599 (p0) REVERT: G 251 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7149 (tm-30) REVERT: G 292 TYR cc_start: 0.8808 (m-80) cc_final: 0.8542 (m-80) REVERT: H 80 LYS cc_start: 0.9049 (mttt) cc_final: 0.8723 (mttp) REVERT: H 145 MET cc_start: 0.7438 (mpp) cc_final: 0.7112 (mpp) REVERT: H 184 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8171 (pt0) REVERT: H 205 VAL cc_start: 0.6373 (t) cc_final: 0.5833 (t) REVERT: H 209 MET cc_start: 0.2411 (mtt) cc_final: 0.1275 (mtp) REVERT: H 232 ASN cc_start: 0.7362 (m-40) cc_final: 0.6412 (p0) REVERT: H 233 LYS cc_start: 0.8314 (tppp) cc_final: 0.7783 (mmmm) REVERT: H 236 LYS cc_start: 0.8613 (tptp) cc_final: 0.8350 (tppt) REVERT: H 251 GLU cc_start: 0.8797 (mm-30) cc_final: 0.7528 (tm-30) REVERT: H 271 ASN cc_start: 0.8642 (t0) cc_final: 0.8271 (t0) REVERT: H 289 ASN cc_start: 0.8348 (p0) cc_final: 0.8064 (p0) REVERT: H 292 TYR cc_start: 0.8517 (m-10) cc_final: 0.8171 (m-80) REVERT: I 73 PHE cc_start: 0.7757 (t80) cc_final: 0.3576 (t80) REVERT: I 80 LYS cc_start: 0.8966 (mttt) cc_final: 0.8696 (mttp) REVERT: I 108 GLU cc_start: 0.7224 (tp30) cc_final: 0.6985 (tp30) REVERT: I 121 TRP cc_start: 0.8633 (m-90) cc_final: 0.8418 (m-90) REVERT: I 145 MET cc_start: 0.7611 (mpp) cc_final: 0.7265 (mpp) REVERT: I 209 MET cc_start: 0.0356 (mtp) cc_final: -0.0167 (mmm) REVERT: I 232 ASN cc_start: 0.7158 (m-40) cc_final: 0.6336 (p0) REVERT: I 233 LYS cc_start: 0.8482 (tppp) cc_final: 0.7793 (mmmm) REVERT: I 251 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7220 (tm-30) REVERT: I 258 GLN cc_start: 0.8948 (tp40) cc_final: 0.8579 (tp40) REVERT: J 73 PHE cc_start: 0.7725 (t80) cc_final: 0.6810 (t80) REVERT: J 108 GLU cc_start: 0.7447 (tp30) cc_final: 0.7059 (tp30) REVERT: J 145 MET cc_start: 0.7682 (mpp) cc_final: 0.7379 (mpp) REVERT: J 220 ARG cc_start: 0.8309 (ptp-170) cc_final: 0.8039 (mtp85) REVERT: J 232 ASN cc_start: 0.7270 (m-40) cc_final: 0.6660 (p0) REVERT: J 233 LYS cc_start: 0.8484 (tppp) cc_final: 0.7925 (mmmm) REVERT: J 251 GLU cc_start: 0.8501 (mm-30) cc_final: 0.6892 (tm-30) REVERT: J 258 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8484 (tp40) REVERT: K 73 PHE cc_start: 0.7774 (t80) cc_final: 0.6773 (t80) REVERT: K 80 LYS cc_start: 0.8849 (mttt) cc_final: 0.8555 (mttp) REVERT: K 108 GLU cc_start: 0.7464 (tp30) cc_final: 0.6948 (tp30) REVERT: K 112 GLU cc_start: 0.7513 (tp30) cc_final: 0.7307 (tp30) REVERT: K 145 MET cc_start: 0.7417 (mpp) cc_final: 0.7207 (mpp) REVERT: K 184 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8300 (mt-10) REVERT: K 232 ASN cc_start: 0.7244 (m-40) cc_final: 0.6596 (p0) REVERT: K 233 LYS cc_start: 0.8396 (tppp) cc_final: 0.7924 (mmmm) REVERT: K 251 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7430 (tm-30) REVERT: K 258 GLN cc_start: 0.9031 (tp40) cc_final: 0.8783 (tp40) REVERT: K 279 MET cc_start: 0.8443 (mtm) cc_final: 0.7908 (mmp) REVERT: K 292 TYR cc_start: 0.8839 (m-10) cc_final: 0.8549 (m-80) REVERT: L 145 MET cc_start: 0.7508 (mpp) cc_final: 0.7287 (mpp) REVERT: L 206 TYR cc_start: 0.5914 (t80) cc_final: 0.5597 (t80) REVERT: L 232 ASN cc_start: 0.7236 (m-40) cc_final: 0.6434 (p0) REVERT: L 233 LYS cc_start: 0.8173 (tppp) cc_final: 0.7804 (mmmm) REVERT: L 251 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7444 (tm-30) REVERT: L 260 ILE cc_start: 0.9058 (mt) cc_final: 0.8730 (mt) REVERT: M 80 LYS cc_start: 0.9008 (mttt) cc_final: 0.8734 (mttp) REVERT: M 101 ASN cc_start: 0.7657 (m110) cc_final: 0.7448 (m110) REVERT: M 114 ARG cc_start: 0.9063 (ttp-170) cc_final: 0.8850 (ttp80) REVERT: M 145 MET cc_start: 0.7431 (mpp) cc_final: 0.6636 (mpp) REVERT: M 200 MET cc_start: 0.7360 (tpp) cc_final: 0.7157 (tpp) REVERT: M 232 ASN cc_start: 0.7280 (m-40) cc_final: 0.6314 (p0) REVERT: M 233 LYS cc_start: 0.8010 (tppp) cc_final: 0.7340 (mmmm) REVERT: M 251 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7460 (tm-30) REVERT: M 258 GLN cc_start: 0.8988 (tp40) cc_final: 0.8565 (tp40) REVERT: N 80 LYS cc_start: 0.9001 (mttt) cc_final: 0.8724 (mttp) REVERT: N 112 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7298 (mt-10) REVERT: N 209 MET cc_start: 0.3207 (mtt) cc_final: 0.2220 (mtp) REVERT: N 232 ASN cc_start: 0.7038 (m-40) cc_final: 0.6314 (p0) REVERT: N 251 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7616 (tm-30) REVERT: N 258 GLN cc_start: 0.8895 (tp40) cc_final: 0.8651 (tp-100) REVERT: O 86 MET cc_start: 0.7655 (tpp) cc_final: 0.6418 (ttm) REVERT: O 145 MET cc_start: 0.7399 (mpp) cc_final: 0.7184 (mpp) REVERT: O 200 MET cc_start: 0.7449 (tpp) cc_final: 0.6711 (mmm) REVERT: O 251 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7096 (tm-30) REVERT: O 258 GLN cc_start: 0.9019 (tp40) cc_final: 0.8582 (tp40) REVERT: O 279 MET cc_start: 0.8400 (mtm) cc_final: 0.7800 (mmp) REVERT: P 80 LYS cc_start: 0.9036 (mttt) cc_final: 0.8807 (mttp) REVERT: P 143 LEU cc_start: 0.9263 (mt) cc_final: 0.8856 (mt) REVERT: P 145 MET cc_start: 0.7425 (mpp) cc_final: 0.6597 (mpp) REVERT: P 169 LEU cc_start: 0.8606 (tp) cc_final: 0.8126 (tp) REVERT: P 173 ASP cc_start: 0.7993 (t0) cc_final: 0.7770 (t0) REVERT: P 232 ASN cc_start: 0.7180 (m-40) cc_final: 0.6340 (p0) REVERT: P 233 LYS cc_start: 0.8097 (tppp) cc_final: 0.7457 (mmmm) REVERT: P 251 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7416 (tm-30) REVERT: P 252 LYS cc_start: 0.8546 (ptpp) cc_final: 0.7944 (tppt) REVERT: P 258 GLN cc_start: 0.9035 (tp40) cc_final: 0.8554 (tp40) REVERT: P 260 ILE cc_start: 0.9095 (mt) cc_final: 0.8813 (mt) REVERT: Q 134 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7915 (mt-10) REVERT: Q 143 LEU cc_start: 0.9332 (mt) cc_final: 0.9020 (mt) REVERT: Q 145 MET cc_start: 0.7316 (mpp) cc_final: 0.6986 (mpp) REVERT: Q 169 LEU cc_start: 0.8468 (tp) cc_final: 0.8094 (tp) REVERT: Q 236 LYS cc_start: 0.8659 (tptp) cc_final: 0.8391 (tppt) REVERT: Q 240 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8411 (tttt) REVERT: Q 251 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7273 (tm-30) REVERT: Q 271 ASN cc_start: 0.8607 (t0) cc_final: 0.8314 (t0) REVERT: R 86 MET cc_start: 0.7083 (tpp) cc_final: 0.6436 (ttm) REVERT: R 232 ASN cc_start: 0.7383 (m-40) cc_final: 0.6590 (p0) REVERT: R 251 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7433 (tm-30) REVERT: R 258 GLN cc_start: 0.9027 (tp40) cc_final: 0.8575 (tp40) REVERT: R 279 MET cc_start: 0.8409 (mtm) cc_final: 0.7759 (mmp) REVERT: R 289 ASN cc_start: 0.8950 (p0) cc_final: 0.8655 (p0) REVERT: R 292 TYR cc_start: 0.8740 (m-10) cc_final: 0.8391 (m-10) outliers start: 5 outliers final: 1 residues processed: 1260 average time/residue: 0.2386 time to fit residues: 467.4772 Evaluate side-chains 1071 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1070 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 399 optimal weight: 5.9990 chunk 29 optimal weight: 0.0570 chunk 171 optimal weight: 0.5980 chunk 286 optimal weight: 0.9990 chunk 77 optimal weight: 0.0060 chunk 316 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 261 optimal weight: 0.0000 chunk 217 optimal weight: 0.2980 chunk 247 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 overall best weight: 0.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 146 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 146 ASN D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 146 ASN ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 262 GLN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN N 81 GLN N 167 GLN O 81 GLN O 146 ASN O 259 GLN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 GLN ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 ASN R 167 GLN R 258 GLN R 262 GLN ** R 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138329 restraints weight = 64338.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143435 restraints weight = 42455.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147161 restraints weight = 31056.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149886 restraints weight = 24389.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.151918 restraints weight = 20222.905| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34326 Z= 0.135 Angle : 0.744 10.107 46422 Z= 0.356 Chirality : 0.045 0.191 5346 Planarity : 0.004 0.082 5940 Dihedral : 10.755 160.580 4842 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4158 helix: 0.65 (0.10), residues: 2484 sheet: -1.05 (0.21), residues: 594 loop : 0.43 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 224 TYR 0.015 0.001 TYR Q 113 PHE 0.019 0.001 PHE N 297 TRP 0.054 0.002 TRP P 83 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00284 (34326) covalent geometry : angle 0.74414 (46422) hydrogen bonds : bond 0.03331 ( 1852) hydrogen bonds : angle 4.35218 ( 5448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1240 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.9328 (mt) cc_final: 0.8984 (mt) REVERT: A 169 LEU cc_start: 0.8242 (tp) cc_final: 0.8042 (tp) REVERT: A 209 MET cc_start: -0.0228 (mtp) cc_final: -0.0712 (mmm) REVERT: A 232 ASN cc_start: 0.7687 (m-40) cc_final: 0.6600 (p0) REVERT: A 233 LYS cc_start: 0.7993 (tppp) cc_final: 0.7375 (mmmm) REVERT: A 251 GLU cc_start: 0.8692 (mm-30) cc_final: 0.7459 (tm-30) REVERT: A 252 LYS cc_start: 0.8546 (ptpp) cc_final: 0.7784 (tppt) REVERT: A 258 GLN cc_start: 0.9110 (tp40) cc_final: 0.8797 (tp40) REVERT: A 279 MET cc_start: 0.8517 (mtt) cc_final: 0.8167 (mtm) REVERT: A 289 ASN cc_start: 0.8450 (p0) cc_final: 0.8178 (p0) REVERT: B 80 LYS cc_start: 0.9000 (mttt) cc_final: 0.8767 (mmtm) REVERT: B 143 LEU cc_start: 0.9105 (mt) cc_final: 0.8818 (mt) REVERT: B 145 MET cc_start: 0.6998 (mpp) cc_final: 0.6144 (mpp) REVERT: B 184 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8159 (mt-10) REVERT: B 256 LEU cc_start: 0.9308 (mm) cc_final: 0.9003 (mm) REVERT: B 260 ILE cc_start: 0.8966 (mt) cc_final: 0.8565 (mt) REVERT: B 289 ASN cc_start: 0.8746 (p0) cc_final: 0.8453 (p0) REVERT: B 292 TYR cc_start: 0.8674 (m-10) cc_final: 0.8368 (m-10) REVERT: C 112 GLU cc_start: 0.8734 (pt0) cc_final: 0.8418 (pt0) REVERT: C 145 MET cc_start: 0.7272 (mpp) cc_final: 0.6932 (mpp) REVERT: C 182 VAL cc_start: 0.8118 (t) cc_final: 0.7902 (t) REVERT: C 184 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8265 (mt-10) REVERT: C 224 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6879 (mpp80) REVERT: C 232 ASN cc_start: 0.7584 (m-40) cc_final: 0.6580 (p0) REVERT: C 233 LYS cc_start: 0.7975 (tppp) cc_final: 0.7436 (mmmm) REVERT: C 258 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8493 (tp40) REVERT: C 260 ILE cc_start: 0.8993 (mt) cc_final: 0.8718 (mt) REVERT: C 279 MET cc_start: 0.8517 (mtm) cc_final: 0.8183 (mmp) REVERT: D 145 MET cc_start: 0.7215 (mpp) cc_final: 0.6788 (mpp) REVERT: D 232 ASN cc_start: 0.7658 (m-40) cc_final: 0.6516 (p0) REVERT: D 235 LYS cc_start: 0.9135 (mttt) cc_final: 0.8771 (mmmt) REVERT: D 251 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7012 (tm-30) REVERT: D 258 GLN cc_start: 0.9074 (tp40) cc_final: 0.8685 (tp40) REVERT: D 271 ASN cc_start: 0.8600 (t0) cc_final: 0.7949 (t0) REVERT: E 80 LYS cc_start: 0.9085 (mttt) cc_final: 0.8850 (mttm) REVERT: E 143 LEU cc_start: 0.9279 (mt) cc_final: 0.8569 (mm) REVERT: E 145 MET cc_start: 0.6601 (mpp) cc_final: 0.6049 (mpp) REVERT: E 232 ASN cc_start: 0.7484 (m-40) cc_final: 0.6310 (p0) REVERT: E 233 LYS cc_start: 0.8123 (tppp) cc_final: 0.7533 (mmmm) REVERT: E 236 LYS cc_start: 0.8613 (tptp) cc_final: 0.8364 (tppt) REVERT: E 240 LYS cc_start: 0.8663 (mttm) cc_final: 0.8192 (ttpt) REVERT: E 251 GLU cc_start: 0.8453 (mm-30) cc_final: 0.6876 (tm-30) REVERT: E 252 LYS cc_start: 0.8452 (ptpp) cc_final: 0.7608 (tppt) REVERT: E 271 ASN cc_start: 0.8856 (t0) cc_final: 0.7575 (p0) REVERT: E 279 MET cc_start: 0.8307 (mtm) cc_final: 0.7870 (tmm) REVERT: E 291 ASP cc_start: 0.7885 (p0) cc_final: 0.7605 (p0) REVERT: F 101 ASN cc_start: 0.7098 (m110) cc_final: 0.6887 (m110) REVERT: F 182 VAL cc_start: 0.7932 (t) cc_final: 0.7617 (t) REVERT: F 184 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8260 (mt-10) REVERT: F 205 VAL cc_start: 0.6726 (t) cc_final: 0.6081 (t) REVERT: F 209 MET cc_start: 0.2756 (mtt) cc_final: 0.1349 (ttm) REVERT: F 232 ASN cc_start: 0.7539 (m-40) cc_final: 0.5945 (p0) REVERT: F 235 LYS cc_start: 0.9146 (mttt) cc_final: 0.8691 (mmmt) REVERT: F 240 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8488 (ptpp) REVERT: F 258 GLN cc_start: 0.9116 (tp40) cc_final: 0.8740 (tp-100) REVERT: G 73 PHE cc_start: 0.7420 (t80) cc_final: 0.6486 (t80) REVERT: G 108 GLU cc_start: 0.7505 (tp30) cc_final: 0.6968 (tp30) REVERT: G 123 ILE cc_start: 0.9239 (pt) cc_final: 0.8912 (pt) REVERT: G 143 LEU cc_start: 0.9101 (mt) cc_final: 0.8573 (mt) REVERT: G 145 MET cc_start: 0.7030 (mpp) cc_final: 0.6431 (mpp) REVERT: G 232 ASN cc_start: 0.7411 (m-40) cc_final: 0.6623 (p0) REVERT: G 233 LYS cc_start: 0.8035 (tppp) cc_final: 0.7700 (mmmm) REVERT: G 251 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7245 (tm-30) REVERT: G 292 TYR cc_start: 0.8755 (m-80) cc_final: 0.8477 (m-80) REVERT: H 76 THR cc_start: 0.8767 (p) cc_final: 0.8084 (p) REVERT: H 80 LYS cc_start: 0.9012 (mttt) cc_final: 0.8768 (mttp) REVERT: H 145 MET cc_start: 0.7090 (mpp) cc_final: 0.6685 (mpp) REVERT: H 182 VAL cc_start: 0.8268 (t) cc_final: 0.8051 (t) REVERT: H 205 VAL cc_start: 0.6573 (t) cc_final: 0.6070 (t) REVERT: H 209 MET cc_start: 0.2232 (mtt) cc_final: 0.1276 (mtp) REVERT: H 232 ASN cc_start: 0.7413 (m-40) cc_final: 0.6452 (p0) REVERT: H 233 LYS cc_start: 0.8117 (tppp) cc_final: 0.7666 (mmmm) REVERT: H 236 LYS cc_start: 0.8642 (tptp) cc_final: 0.8391 (tppt) REVERT: H 251 GLU cc_start: 0.8755 (mm-30) cc_final: 0.7588 (tm-30) REVERT: H 252 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8323 (ptpp) REVERT: H 271 ASN cc_start: 0.8676 (t0) cc_final: 0.8369 (t0) REVERT: H 289 ASN cc_start: 0.8348 (p0) cc_final: 0.7981 (p0) REVERT: H 292 TYR cc_start: 0.8366 (m-10) cc_final: 0.8141 (m-80) REVERT: I 73 PHE cc_start: 0.6897 (t80) cc_final: 0.6118 (t80) REVERT: I 125 ILE cc_start: 0.8252 (pt) cc_final: 0.7546 (pt) REVERT: I 145 MET cc_start: 0.7270 (mpp) cc_final: 0.6836 (mpp) REVERT: I 232 ASN cc_start: 0.7252 (m-40) cc_final: 0.6363 (p0) REVERT: I 233 LYS cc_start: 0.8357 (tppp) cc_final: 0.7838 (mmmm) REVERT: I 251 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7480 (tm-30) REVERT: I 271 ASN cc_start: 0.8977 (t0) cc_final: 0.8770 (t0) REVERT: I 292 TYR cc_start: 0.8800 (m-10) cc_final: 0.8550 (m-10) REVERT: J 73 PHE cc_start: 0.7500 (t80) cc_final: 0.6428 (t80) REVERT: J 108 GLU cc_start: 0.7511 (tp30) cc_final: 0.7174 (tp30) REVERT: J 142 GLU cc_start: 0.8183 (tp30) cc_final: 0.7937 (tp30) REVERT: J 145 MET cc_start: 0.7401 (mpp) cc_final: 0.6998 (mpp) REVERT: J 232 ASN cc_start: 0.7309 (m-40) cc_final: 0.6692 (p0) REVERT: J 233 LYS cc_start: 0.8328 (tppp) cc_final: 0.7837 (mmmm) REVERT: J 251 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7201 (tm-30) REVERT: J 258 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8478 (tp40) REVERT: J 267 LEU cc_start: 0.8160 (mm) cc_final: 0.7904 (mt) REVERT: K 73 PHE cc_start: 0.7525 (t80) cc_final: 0.6417 (t80) REVERT: K 80 LYS cc_start: 0.8857 (mttt) cc_final: 0.8590 (mttp) REVERT: K 108 GLU cc_start: 0.7693 (tp30) cc_final: 0.6999 (tp30) REVERT: K 120 VAL cc_start: 0.9100 (t) cc_final: 0.8861 (m) REVERT: K 135 CYS cc_start: 0.7893 (m) cc_final: 0.7684 (m) REVERT: K 145 MET cc_start: 0.7189 (mpp) cc_final: 0.6736 (mpp) REVERT: K 184 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8247 (mt-10) REVERT: K 209 MET cc_start: 0.0110 (ttt) cc_final: -0.1131 (mmm) REVERT: K 232 ASN cc_start: 0.7346 (m-40) cc_final: 0.6757 (p0) REVERT: K 233 LYS cc_start: 0.8185 (tppp) cc_final: 0.7846 (mmmm) REVERT: K 236 LYS cc_start: 0.8624 (tptp) cc_final: 0.8414 (tppt) REVERT: K 251 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7407 (tm-30) REVERT: K 279 MET cc_start: 0.8506 (mtm) cc_final: 0.7988 (mmp) REVERT: L 112 GLU cc_start: 0.7178 (tp30) cc_final: 0.6975 (tp30) REVERT: L 145 MET cc_start: 0.7472 (mpp) cc_final: 0.7065 (mpp) REVERT: L 232 ASN cc_start: 0.7387 (m-40) cc_final: 0.6636 (p0) REVERT: L 235 LYS cc_start: 0.8908 (mttp) cc_final: 0.8528 (mmmt) REVERT: L 251 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7493 (tm-30) REVERT: L 260 ILE cc_start: 0.8963 (mt) cc_final: 0.8691 (mt) REVERT: M 108 GLU cc_start: 0.8053 (tp30) cc_final: 0.7701 (tp30) REVERT: M 112 GLU cc_start: 0.8472 (pt0) cc_final: 0.7586 (pt0) REVERT: M 114 ARG cc_start: 0.9121 (ttp-170) cc_final: 0.8803 (ttp-170) REVERT: M 145 MET cc_start: 0.6856 (mpp) cc_final: 0.6615 (mpp) REVERT: M 162 ARG cc_start: 0.7570 (ttt90) cc_final: 0.7297 (ttt180) REVERT: M 173 ASP cc_start: 0.8220 (t70) cc_final: 0.7951 (t0) REVERT: M 200 MET cc_start: 0.7213 (tpp) cc_final: 0.6395 (mmm) REVERT: M 251 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7518 (tm-30) REVERT: M 258 GLN cc_start: 0.9026 (tp40) cc_final: 0.8604 (tp40) REVERT: N 80 LYS cc_start: 0.8919 (mttt) cc_final: 0.8695 (mttp) REVERT: N 112 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7316 (mt-10) REVERT: N 174 GLU cc_start: 0.8027 (mp0) cc_final: 0.7522 (mp0) REVERT: N 205 VAL cc_start: 0.6486 (t) cc_final: 0.5921 (t) REVERT: N 209 MET cc_start: 0.2400 (mtt) cc_final: 0.1309 (mtp) REVERT: N 251 GLU cc_start: 0.8646 (mm-30) cc_final: 0.7615 (tm-30) REVERT: N 258 GLN cc_start: 0.8983 (tp40) cc_final: 0.8746 (tp-100) REVERT: O 145 MET cc_start: 0.7127 (mpp) cc_final: 0.6797 (mpp) REVERT: O 200 MET cc_start: 0.7278 (tpp) cc_final: 0.6700 (mmm) REVERT: O 251 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7208 (tm-30) REVERT: O 279 MET cc_start: 0.8434 (mtm) cc_final: 0.7904 (mmp) REVERT: P 80 LYS cc_start: 0.9049 (mttt) cc_final: 0.8813 (mttp) REVERT: P 145 MET cc_start: 0.6716 (mpp) cc_final: 0.5937 (mpp) REVERT: P 174 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7752 (mm-30) REVERT: P 232 ASN cc_start: 0.7230 (m-40) cc_final: 0.6427 (p0) REVERT: P 233 LYS cc_start: 0.8042 (tppp) cc_final: 0.7681 (mmmm) REVERT: P 235 LYS cc_start: 0.9029 (mttt) cc_final: 0.8721 (mmmt) REVERT: P 251 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7501 (tm-30) REVERT: P 252 LYS cc_start: 0.8528 (ptpp) cc_final: 0.7929 (tppt) REVERT: P 258 GLN cc_start: 0.9015 (tp40) cc_final: 0.8550 (tp40) REVERT: P 260 ILE cc_start: 0.9004 (mt) cc_final: 0.8745 (mt) REVERT: P 291 ASP cc_start: 0.8273 (p0) cc_final: 0.8012 (p0) REVERT: Q 143 LEU cc_start: 0.9199 (mt) cc_final: 0.8950 (mt) REVERT: Q 145 MET cc_start: 0.6699 (mpp) cc_final: 0.5749 (mpp) REVERT: Q 229 THR cc_start: 0.6096 (p) cc_final: 0.5225 (t) REVERT: Q 236 LYS cc_start: 0.8724 (tptp) cc_final: 0.8493 (tppt) REVERT: Q 240 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8436 (tttt) REVERT: Q 251 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7382 (tm-30) REVERT: Q 252 LYS cc_start: 0.8446 (ptpp) cc_final: 0.7451 (tppt) REVERT: R 86 MET cc_start: 0.6844 (tpp) cc_final: 0.6323 (ttm) REVERT: R 143 LEU cc_start: 0.9233 (mt) cc_final: 0.9005 (mm) REVERT: R 174 GLU cc_start: 0.8075 (mp0) cc_final: 0.7875 (mp0) REVERT: R 184 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8164 (mt-10) REVERT: R 232 ASN cc_start: 0.7325 (m-40) cc_final: 0.6574 (p0) REVERT: R 236 LYS cc_start: 0.8609 (tptp) cc_final: 0.8406 (tppt) REVERT: R 251 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7443 (tm-30) REVERT: R 289 ASN cc_start: 0.8828 (p0) cc_final: 0.8405 (p0) REVERT: R 292 TYR cc_start: 0.8649 (m-10) cc_final: 0.8406 (m-10) outliers start: 2 outliers final: 1 residues processed: 1240 average time/residue: 0.2392 time to fit residues: 460.9319 Evaluate side-chains 1046 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1045 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 119 optimal weight: 2.9990 chunk 102 optimal weight: 0.0270 chunk 229 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 282 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 146 ASN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 146 ASN K 81 GLN K 271 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 258 GLN M 81 GLN M 146 ASN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN N 81 GLN P 271 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 ASN Q 190 GLN ** Q 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 ASN R 272 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.169904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133966 restraints weight = 65951.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138865 restraints weight = 43521.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.142516 restraints weight = 31937.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.145177 restraints weight = 25122.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147095 restraints weight = 20880.724| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34326 Z= 0.176 Angle : 0.790 9.027 46422 Z= 0.380 Chirality : 0.046 0.236 5346 Planarity : 0.005 0.079 5940 Dihedral : 10.777 153.657 4842 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.11 % Allowed : 1.85 % Favored : 98.04 % 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: -0.01 (0.13), residues: 4158 helix: 0.45 (0.10), residues: 2592 sheet: -1.31 (0.21), residues: 630 loop : 0.16 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 194 TYR 0.018 0.001 TYR J 113 PHE 0.024 0.001 PHE D 88 TRP 0.021 0.001 TRP G 246 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00379 (34326) covalent geometry : angle 0.78955 (46422) hydrogen bonds : bond 0.03490 ( 1852) hydrogen bonds : angle 4.55733 ( 5448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1170 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 THR cc_start: 0.8277 (p) cc_final: 0.7802 (p) REVERT: A 80 LYS cc_start: 0.8938 (mttt) cc_final: 0.8698 (mttp) REVERT: A 143 LEU cc_start: 0.9356 (mt) cc_final: 0.8996 (mt) REVERT: A 145 MET cc_start: 0.7398 (mpp) cc_final: 0.6838 (mpp) REVERT: A 169 LEU cc_start: 0.8274 (tp) cc_final: 0.7934 (tp) REVERT: A 209 MET cc_start: -0.0115 (mtp) cc_final: -0.0561 (mmm) REVERT: A 228 ARG cc_start: 0.6597 (tmt-80) cc_final: 0.6037 (tmt-80) REVERT: A 232 ASN cc_start: 0.7794 (m-40) cc_final: 0.6569 (p0) REVERT: A 233 LYS cc_start: 0.8210 (tppp) cc_final: 0.7993 (mmmm) REVERT: A 235 LYS cc_start: 0.9101 (mttt) cc_final: 0.8688 (mmmt) REVERT: A 251 GLU cc_start: 0.8722 (mm-30) cc_final: 0.7493 (tm-30) REVERT: A 252 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8245 (ptpp) REVERT: A 279 MET cc_start: 0.8505 (mtt) cc_final: 0.8120 (mtm) REVERT: B 80 LYS cc_start: 0.9020 (mttt) cc_final: 0.8791 (mmtm) REVERT: B 101 ASN cc_start: 0.7520 (m110) cc_final: 0.7224 (m-40) REVERT: B 113 TYR cc_start: 0.9337 (t80) cc_final: 0.8998 (t80) REVERT: B 143 LEU cc_start: 0.9291 (mt) cc_final: 0.9081 (mt) REVERT: B 145 MET cc_start: 0.7350 (mpp) cc_final: 0.6819 (mpp) REVERT: B 169 LEU cc_start: 0.8321 (tp) cc_final: 0.8119 (tp) REVERT: B 184 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 190 GLN cc_start: 0.8647 (pt0) cc_final: 0.8402 (pt0) REVERT: B 209 MET cc_start: 0.0326 (tpt) cc_final: 0.0002 (mmm) REVERT: B 232 ASN cc_start: 0.7438 (m-40) cc_final: 0.6463 (p0) REVERT: B 260 ILE cc_start: 0.9013 (mt) cc_final: 0.8667 (mt) REVERT: B 289 ASN cc_start: 0.8781 (p0) cc_final: 0.8453 (p0) REVERT: B 292 TYR cc_start: 0.8721 (m-10) cc_final: 0.8350 (m-10) REVERT: C 112 GLU cc_start: 0.8794 (pt0) cc_final: 0.8554 (pt0) REVERT: C 145 MET cc_start: 0.7013 (mpp) cc_final: 0.5678 (mpp) REVERT: C 184 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8270 (mt-10) REVERT: C 232 ASN cc_start: 0.7648 (m-40) cc_final: 0.6545 (p0) REVERT: C 233 LYS cc_start: 0.8160 (tppp) cc_final: 0.7596 (mmmm) REVERT: C 258 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8472 (tp40) REVERT: D 122 MET cc_start: 0.7221 (tmm) cc_final: 0.6893 (tmm) REVERT: D 145 MET cc_start: 0.7407 (mpp) cc_final: 0.7056 (mpp) REVERT: D 209 MET cc_start: -0.0450 (tpt) cc_final: -0.0849 (mmm) REVERT: D 232 ASN cc_start: 0.7666 (m-40) cc_final: 0.6439 (p0) REVERT: D 235 LYS cc_start: 0.9182 (mttt) cc_final: 0.8799 (mmmt) REVERT: D 251 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7052 (tm-30) REVERT: D 258 GLN cc_start: 0.9104 (tp40) cc_final: 0.8724 (tp40) REVERT: D 271 ASN cc_start: 0.8609 (t0) cc_final: 0.7910 (t0) REVERT: E 80 LYS cc_start: 0.9027 (mttt) cc_final: 0.8822 (mttm) REVERT: E 232 ASN cc_start: 0.7510 (m-40) cc_final: 0.6229 (p0) REVERT: E 233 LYS cc_start: 0.8308 (tppp) cc_final: 0.7635 (mmmm) REVERT: E 240 LYS cc_start: 0.8619 (mttm) cc_final: 0.8164 (ttpt) REVERT: E 252 LYS cc_start: 0.8441 (ptpp) cc_final: 0.7926 (tppt) REVERT: E 258 GLN cc_start: 0.9074 (tp40) cc_final: 0.8621 (tp-100) REVERT: E 271 ASN cc_start: 0.8764 (t0) cc_final: 0.7935 (t0) REVERT: E 279 MET cc_start: 0.8341 (mtm) cc_final: 0.8041 (tmm) REVERT: E 292 TYR cc_start: 0.8430 (m-80) cc_final: 0.8138 (m-80) REVERT: F 80 LYS cc_start: 0.8983 (mttt) cc_final: 0.8756 (mmtm) REVERT: F 101 ASN cc_start: 0.7292 (m110) cc_final: 0.7040 (m110) REVERT: F 174 GLU cc_start: 0.7985 (tt0) cc_final: 0.7600 (tt0) REVERT: F 182 VAL cc_start: 0.8027 (t) cc_final: 0.7762 (t) REVERT: F 184 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8227 (mt-10) REVERT: F 209 MET cc_start: 0.2588 (mtt) cc_final: 0.0782 (ttm) REVERT: F 232 ASN cc_start: 0.7652 (m-40) cc_final: 0.5962 (p0) REVERT: F 235 LYS cc_start: 0.9130 (mttt) cc_final: 0.8666 (mmmt) REVERT: G 73 PHE cc_start: 0.7617 (t80) cc_final: 0.6740 (t80) REVERT: G 80 LYS cc_start: 0.8906 (mttt) cc_final: 0.8634 (mttp) REVERT: G 108 GLU cc_start: 0.7593 (tp30) cc_final: 0.7075 (tp30) REVERT: G 143 LEU cc_start: 0.9290 (mt) cc_final: 0.8655 (mm) REVERT: G 145 MET cc_start: 0.7147 (mpp) cc_final: 0.6556 (mpp) REVERT: G 184 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8066 (mt-10) REVERT: G 232 ASN cc_start: 0.7531 (m-40) cc_final: 0.6622 (p0) REVERT: G 233 LYS cc_start: 0.8238 (tppp) cc_final: 0.7827 (mmmm) REVERT: G 235 LYS cc_start: 0.8802 (mttt) cc_final: 0.8584 (ptpp) REVERT: G 251 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7305 (tm-30) REVERT: G 258 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8531 (tp-100) REVERT: G 292 TYR cc_start: 0.8758 (m-80) cc_final: 0.8511 (m-80) REVERT: H 76 THR cc_start: 0.8661 (p) cc_final: 0.8119 (p) REVERT: H 80 LYS cc_start: 0.8995 (mttt) cc_final: 0.8728 (mttp) REVERT: H 145 MET cc_start: 0.7383 (mpp) cc_final: 0.7002 (mpp) REVERT: H 167 GLN cc_start: 0.7363 (pp30) cc_final: 0.7163 (pp30) REVERT: H 169 LEU cc_start: 0.8371 (tp) cc_final: 0.8137 (tp) REVERT: H 182 VAL cc_start: 0.8358 (t) cc_final: 0.8124 (t) REVERT: H 184 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8210 (pt0) REVERT: H 209 MET cc_start: 0.2299 (mtt) cc_final: 0.1172 (mtp) REVERT: H 232 ASN cc_start: 0.7411 (m-40) cc_final: 0.6377 (p0) REVERT: H 233 LYS cc_start: 0.8195 (tppp) cc_final: 0.7732 (mmmm) REVERT: H 236 LYS cc_start: 0.8621 (tptp) cc_final: 0.8382 (tppt) REVERT: H 251 GLU cc_start: 0.8829 (mm-30) cc_final: 0.7621 (tm-30) REVERT: H 252 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8342 (ptpp) REVERT: H 292 TYR cc_start: 0.8472 (m-10) cc_final: 0.8237 (m-10) REVERT: I 112 GLU cc_start: 0.8023 (pt0) cc_final: 0.7536 (pt0) REVERT: I 145 MET cc_start: 0.7440 (mpp) cc_final: 0.6905 (mpp) REVERT: I 174 GLU cc_start: 0.8554 (pm20) cc_final: 0.8220 (pt0) REVERT: I 232 ASN cc_start: 0.7383 (m-40) cc_final: 0.6494 (p0) REVERT: I 233 LYS cc_start: 0.8436 (tppp) cc_final: 0.7919 (mmmm) REVERT: I 251 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7269 (tm-30) REVERT: I 258 GLN cc_start: 0.8733 (tp40) cc_final: 0.8411 (mm-40) REVERT: I 271 ASN cc_start: 0.9034 (t0) cc_final: 0.8819 (t0) REVERT: I 292 TYR cc_start: 0.8735 (m-10) cc_final: 0.8489 (m-10) REVERT: J 73 PHE cc_start: 0.7949 (t80) cc_final: 0.6905 (t80) REVERT: J 108 GLU cc_start: 0.7695 (tp30) cc_final: 0.7022 (tp30) REVERT: J 145 MET cc_start: 0.7531 (mpp) cc_final: 0.7117 (mpp) REVERT: J 232 ASN cc_start: 0.7431 (m-40) cc_final: 0.6687 (p0) REVERT: J 233 LYS cc_start: 0.8340 (tppp) cc_final: 0.7936 (mmmm) REVERT: J 251 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7010 (tm-30) REVERT: J 258 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8545 (tp40) REVERT: J 289 ASN cc_start: 0.8363 (p0) cc_final: 0.7849 (p0) REVERT: J 292 TYR cc_start: 0.8517 (m-10) cc_final: 0.8270 (m-10) REVERT: K 73 PHE cc_start: 0.7932 (t80) cc_final: 0.6915 (t80) REVERT: K 80 LYS cc_start: 0.8906 (mttt) cc_final: 0.8643 (mttp) REVERT: K 108 GLU cc_start: 0.7804 (tp30) cc_final: 0.7072 (tp30) REVERT: K 142 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7728 (mm-30) REVERT: K 145 MET cc_start: 0.7371 (mpp) cc_final: 0.7009 (mpp) REVERT: K 184 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8257 (mt-10) REVERT: K 209 MET cc_start: 0.0136 (ttt) cc_final: -0.0525 (ttt) REVERT: K 232 ASN cc_start: 0.7336 (m-40) cc_final: 0.6601 (p0) REVERT: K 233 LYS cc_start: 0.8325 (tppp) cc_final: 0.7882 (mmmm) REVERT: K 236 LYS cc_start: 0.8661 (tptp) cc_final: 0.8416 (tppt) REVERT: K 251 GLU cc_start: 0.8653 (mm-30) cc_final: 0.7400 (tm-30) REVERT: K 279 MET cc_start: 0.8551 (mtm) cc_final: 0.7993 (mmp) REVERT: L 112 GLU cc_start: 0.7290 (tp30) cc_final: 0.7081 (tp30) REVERT: L 145 MET cc_start: 0.7422 (mpp) cc_final: 0.6697 (mpp) REVERT: L 184 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8376 (mt-10) REVERT: L 193 THR cc_start: 0.8229 (m) cc_final: 0.7935 (t) REVERT: L 232 ASN cc_start: 0.7383 (m-40) cc_final: 0.6430 (p0) REVERT: L 251 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7467 (tm-30) REVERT: L 260 ILE cc_start: 0.8985 (mt) cc_final: 0.8664 (mt) REVERT: L 279 MET cc_start: 0.8488 (mtm) cc_final: 0.8271 (tmm) REVERT: M 80 LYS cc_start: 0.8952 (mttt) cc_final: 0.8697 (mttp) REVERT: M 114 ARG cc_start: 0.9202 (ttp-170) cc_final: 0.8347 (ttp80) REVERT: M 122 MET cc_start: 0.7357 (tmm) cc_final: 0.6898 (tmm) REVERT: M 145 MET cc_start: 0.7120 (mpp) cc_final: 0.6787 (mpp) REVERT: M 200 MET cc_start: 0.7372 (tpp) cc_final: 0.6491 (mmm) REVERT: M 251 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7502 (tm-30) REVERT: M 258 GLN cc_start: 0.9056 (tp40) cc_final: 0.8618 (tp40) REVERT: M 298 ARG cc_start: 0.8751 (mpt180) cc_final: 0.8378 (mmt90) REVERT: N 80 LYS cc_start: 0.8919 (mttt) cc_final: 0.8692 (mttp) REVERT: N 112 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7261 (mt-10) REVERT: N 132 VAL cc_start: 0.7864 (t) cc_final: 0.7629 (t) REVERT: N 209 MET cc_start: 0.3075 (mtt) cc_final: 0.1744 (mtp) REVERT: N 220 ARG cc_start: 0.6134 (mtp180) cc_final: 0.5618 (mtp180) REVERT: N 232 ASN cc_start: 0.7135 (m-40) cc_final: 0.6528 (p0) REVERT: N 251 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7567 (tm-30) REVERT: N 258 GLN cc_start: 0.9011 (tp40) cc_final: 0.8747 (tp-100) REVERT: O 112 GLU cc_start: 0.8550 (pt0) cc_final: 0.7828 (pt0) REVERT: O 145 MET cc_start: 0.7322 (mpp) cc_final: 0.7067 (mpp) REVERT: O 184 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8279 (mt-10) REVERT: O 200 MET cc_start: 0.7372 (tpp) cc_final: 0.6800 (mmm) REVERT: O 251 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7125 (tm-30) REVERT: O 258 GLN cc_start: 0.8954 (tp40) cc_final: 0.8659 (tp-100) REVERT: P 80 LYS cc_start: 0.9029 (mttt) cc_final: 0.8807 (mttp) REVERT: P 108 GLU cc_start: 0.8132 (tp30) cc_final: 0.7843 (tp30) REVERT: P 112 GLU cc_start: 0.8798 (pt0) cc_final: 0.7702 (pt0) REVERT: P 122 MET cc_start: 0.7368 (tmm) cc_final: 0.7167 (tmm) REVERT: P 143 LEU cc_start: 0.9226 (mt) cc_final: 0.8801 (mt) REVERT: P 145 MET cc_start: 0.6921 (mpp) cc_final: 0.6392 (mpp) REVERT: P 182 VAL cc_start: 0.8438 (t) cc_final: 0.8220 (t) REVERT: P 232 ASN cc_start: 0.7357 (m-40) cc_final: 0.6224 (p0) REVERT: P 233 LYS cc_start: 0.8183 (tppp) cc_final: 0.7662 (mmmm) REVERT: P 235 LYS cc_start: 0.9090 (mttt) cc_final: 0.8768 (mmmt) REVERT: P 251 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7521 (tm-30) REVERT: P 258 GLN cc_start: 0.9023 (tp40) cc_final: 0.8576 (tp40) REVERT: P 260 ILE cc_start: 0.9060 (mt) cc_final: 0.8840 (mt) REVERT: Q 108 GLU cc_start: 0.8122 (tp30) cc_final: 0.7842 (tp30) REVERT: Q 112 GLU cc_start: 0.8595 (pt0) cc_final: 0.7843 (pt0) REVERT: Q 143 LEU cc_start: 0.9252 (mt) cc_final: 0.8977 (mt) REVERT: Q 145 MET cc_start: 0.7112 (mpp) cc_final: 0.6228 (mpp) REVERT: Q 184 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8266 (mt-10) REVERT: Q 209 MET cc_start: 0.0259 (ttt) cc_final: -0.0509 (mmm) REVERT: Q 228 ARG cc_start: 0.7804 (ttp80) cc_final: 0.6297 (tmt170) REVERT: Q 229 THR cc_start: 0.6412 (p) cc_final: 0.4916 (t) REVERT: Q 232 ASN cc_start: 0.7344 (m-40) cc_final: 0.6456 (p0) REVERT: Q 236 LYS cc_start: 0.8710 (tptp) cc_final: 0.8485 (tppt) REVERT: Q 240 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8453 (tttt) REVERT: Q 251 GLU cc_start: 0.8642 (mm-30) cc_final: 0.7434 (tm-30) REVERT: Q 252 LYS cc_start: 0.8511 (ptpp) cc_final: 0.7509 (tppt) REVERT: Q 294 ARG cc_start: 0.9189 (mmm160) cc_final: 0.8956 (mmm160) REVERT: R 86 MET cc_start: 0.6978 (tpp) cc_final: 0.6310 (ttm) REVERT: R 143 LEU cc_start: 0.9278 (mt) cc_final: 0.9049 (mt) REVERT: R 145 MET cc_start: 0.7200 (mpp) cc_final: 0.6731 (mpp) REVERT: R 167 GLN cc_start: 0.6738 (mm110) cc_final: 0.6526 (mp10) REVERT: R 184 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8182 (mt-10) REVERT: R 232 ASN cc_start: 0.7238 (m-40) cc_final: 0.6558 (p0) REVERT: R 251 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7437 (tm-30) REVERT: R 289 ASN cc_start: 0.8851 (p0) cc_final: 0.8475 (p0) REVERT: R 292 TYR cc_start: 0.8726 (m-10) cc_final: 0.8406 (m-10) outliers start: 4 outliers final: 0 residues processed: 1171 average time/residue: 0.2403 time to fit residues: 438.7982 Evaluate side-chains 1042 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1042 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 255 optimal weight: 0.5980 chunk 392 optimal weight: 0.7980 chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 286 optimal weight: 0.2980 chunk 313 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 chunk 373 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 146 ASN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN F 258 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 146 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 146 ASN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN P 167 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 ASN ** Q 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 GLN R 262 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.172067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.136137 restraints weight = 65277.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141202 restraints weight = 43617.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144857 restraints weight = 32001.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147481 restraints weight = 25208.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149464 restraints weight = 20993.008| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 34326 Z= 0.145 Angle : 0.758 9.263 46422 Z= 0.363 Chirality : 0.045 0.221 5346 Planarity : 0.004 0.043 5940 Dihedral : 10.337 146.006 4842 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4158 helix: 0.63 (0.10), residues: 2592 sheet: -1.31 (0.20), residues: 630 loop : 0.25 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 275 TYR 0.017 0.001 TYR J 113 PHE 0.033 0.001 PHE N 297 TRP 0.050 0.002 TRP K 246 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00320 (34326) covalent geometry : angle 0.75770 (46422) hydrogen bonds : bond 0.03334 ( 1852) hydrogen bonds : angle 4.37462 ( 5448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1182 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 THR cc_start: 0.8287 (p) cc_final: 0.7869 (p) REVERT: A 80 LYS cc_start: 0.8905 (mttt) cc_final: 0.8675 (mttp) REVERT: A 143 LEU cc_start: 0.9369 (mt) cc_final: 0.9001 (mt) REVERT: A 145 MET cc_start: 0.7372 (mpp) cc_final: 0.6840 (mpp) REVERT: A 169 LEU cc_start: 0.8365 (tp) cc_final: 0.7972 (tp) REVERT: A 209 MET cc_start: -0.0239 (mtp) cc_final: -0.0533 (mmm) REVERT: A 228 ARG cc_start: 0.6827 (tmt-80) cc_final: 0.6091 (tmt-80) REVERT: A 232 ASN cc_start: 0.7721 (m-40) cc_final: 0.6453 (p0) REVERT: A 233 LYS cc_start: 0.8095 (tppp) cc_final: 0.7537 (mmmm) REVERT: A 251 GLU cc_start: 0.8687 (mm-30) cc_final: 0.7456 (tm-30) REVERT: A 252 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8230 (ptpp) REVERT: A 258 GLN cc_start: 0.8957 (tp40) cc_final: 0.8552 (mm-40) REVERT: A 279 MET cc_start: 0.8528 (mtt) cc_final: 0.8149 (mtm) REVERT: B 101 ASN cc_start: 0.7402 (m110) cc_final: 0.7169 (m-40) REVERT: B 143 LEU cc_start: 0.9272 (mt) cc_final: 0.8947 (mt) REVERT: B 145 MET cc_start: 0.6971 (mpp) cc_final: 0.6498 (mpp) REVERT: B 184 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 190 GLN cc_start: 0.8589 (pt0) cc_final: 0.8275 (pt0) REVERT: B 209 MET cc_start: 0.0204 (tpt) cc_final: -0.0086 (mmm) REVERT: B 232 ASN cc_start: 0.7417 (m-40) cc_final: 0.6340 (p0) REVERT: C 112 GLU cc_start: 0.8760 (pt0) cc_final: 0.8410 (pt0) REVERT: C 142 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 159 LEU cc_start: 0.8921 (mt) cc_final: 0.8688 (mt) REVERT: C 184 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8272 (mt-10) REVERT: C 209 MET cc_start: -0.1690 (mmm) cc_final: -0.1956 (mmm) REVERT: C 224 ARG cc_start: 0.7624 (mtt180) cc_final: 0.6953 (mpp80) REVERT: C 232 ASN cc_start: 0.7516 (m-40) cc_final: 0.6424 (p0) REVERT: C 233 LYS cc_start: 0.7890 (tppp) cc_final: 0.7372 (mmmm) REVERT: C 258 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8509 (tp40) REVERT: C 271 ASN cc_start: 0.8622 (t0) cc_final: 0.8408 (t0) REVERT: D 122 MET cc_start: 0.7335 (tmm) cc_final: 0.7039 (tmm) REVERT: D 145 MET cc_start: 0.7190 (mpp) cc_final: 0.6825 (mpp) REVERT: D 209 MET cc_start: -0.0417 (tpt) cc_final: -0.0834 (mmm) REVERT: D 232 ASN cc_start: 0.7672 (m-40) cc_final: 0.6398 (p0) REVERT: D 235 LYS cc_start: 0.9184 (mttt) cc_final: 0.8773 (mmmt) REVERT: D 251 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7070 (tm-30) REVERT: D 258 GLN cc_start: 0.9103 (tp40) cc_final: 0.8663 (tp40) REVERT: D 271 ASN cc_start: 0.8575 (t0) cc_final: 0.7867 (p0) REVERT: D 298 ARG cc_start: 0.8528 (mpt180) cc_final: 0.7863 (mmt-90) REVERT: E 145 MET cc_start: 0.6778 (mpp) cc_final: 0.6211 (mpp) REVERT: E 232 ASN cc_start: 0.7486 (m-40) cc_final: 0.6114 (p0) REVERT: E 233 LYS cc_start: 0.8327 (tppp) cc_final: 0.7628 (mmmm) REVERT: E 236 LYS cc_start: 0.8570 (tptp) cc_final: 0.8364 (tppt) REVERT: E 240 LYS cc_start: 0.8565 (mttm) cc_final: 0.8041 (ttpt) REVERT: E 251 GLU cc_start: 0.8477 (mm-30) cc_final: 0.6895 (tm-30) REVERT: E 252 LYS cc_start: 0.8447 (ptpp) cc_final: 0.7581 (tppt) REVERT: E 275 ARG cc_start: 0.7859 (mpp-170) cc_final: 0.7642 (mmm-85) REVERT: E 279 MET cc_start: 0.8409 (mtm) cc_final: 0.8206 (tmm) REVERT: E 292 TYR cc_start: 0.8370 (m-80) cc_final: 0.8029 (m-80) REVERT: F 80 LYS cc_start: 0.8918 (mttt) cc_final: 0.8691 (mmtm) REVERT: F 173 ASP cc_start: 0.8417 (t0) cc_final: 0.7169 (m-30) REVERT: F 174 GLU cc_start: 0.8056 (tt0) cc_final: 0.7790 (tm-30) REVERT: F 182 VAL cc_start: 0.7931 (t) cc_final: 0.7650 (t) REVERT: F 184 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8241 (mt-10) REVERT: F 190 GLN cc_start: 0.8797 (pt0) cc_final: 0.8551 (pt0) REVERT: F 209 MET cc_start: 0.2563 (mtt) cc_final: 0.0375 (ttt) REVERT: F 232 ASN cc_start: 0.7583 (m-40) cc_final: 0.6069 (p0) REVERT: F 235 LYS cc_start: 0.9090 (mttt) cc_final: 0.8593 (mmmt) REVERT: F 258 GLN cc_start: 0.8722 (tp40) cc_final: 0.8486 (tp-100) REVERT: G 73 PHE cc_start: 0.7510 (t80) cc_final: 0.6564 (t80) REVERT: G 80 LYS cc_start: 0.8898 (mttt) cc_final: 0.8645 (mttp) REVERT: G 108 GLU cc_start: 0.7556 (tp30) cc_final: 0.7004 (tp30) REVERT: G 184 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8163 (mt-10) REVERT: G 232 ASN cc_start: 0.7298 (m-40) cc_final: 0.6493 (p0) REVERT: G 233 LYS cc_start: 0.8176 (tppp) cc_final: 0.7781 (mmmm) REVERT: G 251 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7316 (tm-30) REVERT: G 258 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8522 (tp-100) REVERT: H 76 THR cc_start: 0.8605 (p) cc_final: 0.8081 (p) REVERT: H 80 LYS cc_start: 0.8978 (mttt) cc_final: 0.8739 (mttp) REVERT: H 145 MET cc_start: 0.7282 (mpp) cc_final: 0.6931 (mpp) REVERT: H 167 GLN cc_start: 0.7264 (pp30) cc_final: 0.7054 (pp30) REVERT: H 182 VAL cc_start: 0.8319 (t) cc_final: 0.8085 (t) REVERT: H 184 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8131 (pt0) REVERT: H 209 MET cc_start: 0.2115 (mtt) cc_final: 0.1064 (mtp) REVERT: H 232 ASN cc_start: 0.7456 (m-40) cc_final: 0.6278 (p0) REVERT: H 233 LYS cc_start: 0.8175 (tppp) cc_final: 0.7629 (mmmm) REVERT: H 236 LYS cc_start: 0.8572 (tptp) cc_final: 0.8357 (tppt) REVERT: H 251 GLU cc_start: 0.8761 (mm-30) cc_final: 0.7528 (tm-30) REVERT: H 252 LYS cc_start: 0.8665 (ptpp) cc_final: 0.7859 (tppt) REVERT: H 292 TYR cc_start: 0.8357 (m-10) cc_final: 0.8152 (m-10) REVERT: I 76 THR cc_start: 0.7973 (p) cc_final: 0.7698 (p) REVERT: I 80 LYS cc_start: 0.8932 (mttt) cc_final: 0.8722 (mttp) REVERT: I 112 GLU cc_start: 0.8108 (pt0) cc_final: 0.7617 (pt0) REVERT: I 125 ILE cc_start: 0.8263 (pt) cc_final: 0.7756 (pt) REVERT: I 145 MET cc_start: 0.7404 (mpp) cc_final: 0.6977 (mpp) REVERT: I 190 GLN cc_start: 0.7974 (pp30) cc_final: 0.7622 (pp30) REVERT: I 232 ASN cc_start: 0.7335 (m-40) cc_final: 0.6397 (p0) REVERT: I 233 LYS cc_start: 0.8329 (tppp) cc_final: 0.7923 (mmmm) REVERT: I 251 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7299 (tm-30) REVERT: I 258 GLN cc_start: 0.8778 (tp40) cc_final: 0.8549 (mm-40) REVERT: I 292 TYR cc_start: 0.8730 (m-10) cc_final: 0.8487 (m-10) REVERT: J 73 PHE cc_start: 0.7815 (t80) cc_final: 0.6887 (t80) REVERT: J 86 MET cc_start: 0.7356 (ttm) cc_final: 0.6721 (ttm) REVERT: J 108 GLU cc_start: 0.7615 (tp30) cc_final: 0.6968 (tp30) REVERT: J 112 GLU cc_start: 0.7527 (tp30) cc_final: 0.7208 (tp30) REVERT: J 145 MET cc_start: 0.7427 (mpp) cc_final: 0.7085 (mpp) REVERT: J 232 ASN cc_start: 0.7500 (m-40) cc_final: 0.6644 (p0) REVERT: J 233 LYS cc_start: 0.8241 (tppp) cc_final: 0.7843 (mmmm) REVERT: J 251 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7200 (tm-30) REVERT: J 258 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8500 (tp40) REVERT: J 289 ASN cc_start: 0.8284 (p0) cc_final: 0.7915 (p0) REVERT: K 73 PHE cc_start: 0.7504 (t80) cc_final: 0.6683 (t80) REVERT: K 80 LYS cc_start: 0.8876 (mttt) cc_final: 0.8644 (mttp) REVERT: K 108 GLU cc_start: 0.7774 (tp30) cc_final: 0.7040 (tp30) REVERT: K 145 MET cc_start: 0.7353 (mpp) cc_final: 0.6940 (mpp) REVERT: K 232 ASN cc_start: 0.7260 (m-40) cc_final: 0.6525 (p0) REVERT: K 233 LYS cc_start: 0.8252 (tppp) cc_final: 0.7822 (mmmm) REVERT: K 236 LYS cc_start: 0.8569 (tptp) cc_final: 0.8331 (tppt) REVERT: K 251 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7356 (tm-30) REVERT: K 279 MET cc_start: 0.8493 (mtm) cc_final: 0.7969 (mmp) REVERT: L 125 ILE cc_start: 0.8187 (pt) cc_final: 0.7433 (pt) REVERT: L 145 MET cc_start: 0.7504 (mpp) cc_final: 0.6708 (mpp) REVERT: L 232 ASN cc_start: 0.7452 (m-40) cc_final: 0.6421 (p0) REVERT: L 251 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7410 (tm-30) REVERT: L 252 LYS cc_start: 0.8474 (ptpp) cc_final: 0.7961 (tppt) REVERT: L 260 ILE cc_start: 0.9006 (mt) cc_final: 0.8680 (mt) REVERT: L 279 MET cc_start: 0.8474 (mtm) cc_final: 0.7887 (mmp) REVERT: M 108 GLU cc_start: 0.8120 (tp30) cc_final: 0.7771 (tp30) REVERT: M 112 GLU cc_start: 0.8574 (pt0) cc_final: 0.7662 (pt0) REVERT: M 145 MET cc_start: 0.7051 (mpp) cc_final: 0.6433 (mpp) REVERT: M 200 MET cc_start: 0.7293 (tpp) cc_final: 0.6606 (mmm) REVERT: M 232 ASN cc_start: 0.7439 (m-40) cc_final: 0.6317 (p0) REVERT: M 251 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7542 (tm-30) REVERT: M 258 GLN cc_start: 0.9052 (tp40) cc_final: 0.8624 (tp40) REVERT: N 80 LYS cc_start: 0.8914 (mttt) cc_final: 0.8704 (mttp) REVERT: N 112 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7117 (mt-10) REVERT: N 209 MET cc_start: 0.2900 (mtt) cc_final: 0.1641 (mtp) REVERT: N 232 ASN cc_start: 0.7264 (m-40) cc_final: 0.6683 (p0) REVERT: N 251 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7493 (tm-30) REVERT: N 258 GLN cc_start: 0.8950 (tp40) cc_final: 0.8602 (tp-100) REVERT: N 260 ILE cc_start: 0.9197 (mt) cc_final: 0.8984 (mt) REVERT: N 289 ASN cc_start: 0.8563 (p0) cc_final: 0.8100 (p0) REVERT: N 292 TYR cc_start: 0.8273 (m-10) cc_final: 0.7833 (m-80) REVERT: O 112 GLU cc_start: 0.8520 (pt0) cc_final: 0.7746 (pt0) REVERT: O 145 MET cc_start: 0.7240 (mpp) cc_final: 0.6870 (mpp) REVERT: O 184 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8213 (mt-10) REVERT: O 200 MET cc_start: 0.7406 (tpp) cc_final: 0.6889 (mmm) REVERT: O 251 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7104 (tm-30) REVERT: O 258 GLN cc_start: 0.8895 (tp40) cc_final: 0.8343 (mm-40) REVERT: P 101 ASN cc_start: 0.7458 (m110) cc_final: 0.7253 (m-40) REVERT: P 143 LEU cc_start: 0.9204 (mt) cc_final: 0.8601 (mt) REVERT: P 145 MET cc_start: 0.6982 (mpp) cc_final: 0.6331 (mpp) REVERT: P 182 VAL cc_start: 0.8330 (t) cc_final: 0.8119 (t) REVERT: P 232 ASN cc_start: 0.7343 (m-40) cc_final: 0.6384 (p0) REVERT: P 233 LYS cc_start: 0.8128 (tppp) cc_final: 0.7855 (mmmm) REVERT: P 235 LYS cc_start: 0.9064 (mttt) cc_final: 0.8719 (mmmt) REVERT: P 251 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7474 (tm-30) REVERT: P 252 LYS cc_start: 0.8707 (ptpp) cc_final: 0.7845 (tppt) REVERT: P 258 GLN cc_start: 0.9017 (tp40) cc_final: 0.8533 (tp40) REVERT: P 271 ASN cc_start: 0.9147 (t0) cc_final: 0.8919 (p0) REVERT: Q 108 GLU cc_start: 0.8115 (tp30) cc_final: 0.7813 (tp30) REVERT: Q 112 GLU cc_start: 0.8559 (pt0) cc_final: 0.7891 (pt0) REVERT: Q 143 LEU cc_start: 0.9246 (mt) cc_final: 0.8833 (mt) REVERT: Q 145 MET cc_start: 0.6882 (mpp) cc_final: 0.6051 (mpp) REVERT: Q 209 MET cc_start: 0.0110 (ttt) cc_final: -0.0976 (mmm) REVERT: Q 228 ARG cc_start: 0.7842 (ttp80) cc_final: 0.6953 (tmt-80) REVERT: Q 232 ASN cc_start: 0.7313 (m-40) cc_final: 0.6463 (p0) REVERT: Q 236 LYS cc_start: 0.8708 (tptp) cc_final: 0.8501 (tppt) REVERT: Q 240 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8438 (tttt) REVERT: Q 251 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7428 (tm-30) REVERT: Q 252 LYS cc_start: 0.8507 (ptpp) cc_final: 0.7470 (tppt) REVERT: R 86 MET cc_start: 0.6965 (tpp) cc_final: 0.6278 (ttm) REVERT: R 143 LEU cc_start: 0.9253 (mt) cc_final: 0.8950 (mm) REVERT: R 145 MET cc_start: 0.6927 (mpp) cc_final: 0.6615 (mpp) REVERT: R 184 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8074 (mt-10) REVERT: R 232 ASN cc_start: 0.7252 (m-40) cc_final: 0.6693 (p0) REVERT: R 251 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7525 (tm-30) REVERT: R 258 GLN cc_start: 0.8770 (tp40) cc_final: 0.8220 (mm-40) REVERT: R 289 ASN cc_start: 0.8813 (p0) cc_final: 0.8414 (p0) REVERT: R 292 TYR cc_start: 0.8683 (m-10) cc_final: 0.8428 (m-10) outliers start: 1 outliers final: 1 residues processed: 1183 average time/residue: 0.2381 time to fit residues: 438.4631 Evaluate side-chains 1046 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1045 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 233 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 402 optimal weight: 6.9990 chunk 405 optimal weight: 10.0000 chunk 397 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 82 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 262 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** F 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 ASN J 146 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 146 ASN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN N 81 GLN N 146 ASN ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 ASN Q 167 GLN ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.174763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139385 restraints weight = 63683.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144304 restraints weight = 42651.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147837 restraints weight = 31390.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.150451 restraints weight = 24833.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.152379 restraints weight = 20665.988| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34326 Z= 0.140 Angle : 0.763 12.296 46422 Z= 0.369 Chirality : 0.045 0.232 5346 Planarity : 0.004 0.087 5940 Dihedral : 10.076 151.025 4842 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.06 % Allowed : 1.01 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4158 helix: 0.76 (0.10), residues: 2556 sheet: -1.14 (0.21), residues: 594 loop : 0.31 (0.22), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 194 TYR 0.018 0.001 TYR B 113 PHE 0.024 0.001 PHE H 297 TRP 0.028 0.001 TRP K 246 HIS 0.010 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00305 (34326) covalent geometry : angle 0.76321 (46422) hydrogen bonds : bond 0.03226 ( 1852) hydrogen bonds : angle 4.32132 ( 5448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1168 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 THR cc_start: 0.8333 (p) cc_final: 0.7936 (p) REVERT: A 80 LYS cc_start: 0.8887 (mttt) cc_final: 0.8657 (mttp) REVERT: A 112 GLU cc_start: 0.9173 (pm20) cc_final: 0.8973 (pm20) REVERT: A 143 LEU cc_start: 0.9404 (mt) cc_final: 0.9039 (mt) REVERT: A 145 MET cc_start: 0.7387 (mpp) cc_final: 0.6831 (mpp) REVERT: A 169 LEU cc_start: 0.8106 (tp) cc_final: 0.7815 (tp) REVERT: A 209 MET cc_start: -0.0151 (mtp) cc_final: -0.0519 (mmm) REVERT: A 228 ARG cc_start: 0.6807 (tmt-80) cc_final: 0.6030 (tmt-80) REVERT: A 229 THR cc_start: 0.6213 (p) cc_final: 0.5713 (m) REVERT: A 232 ASN cc_start: 0.7621 (m-40) cc_final: 0.6400 (p0) REVERT: A 233 LYS cc_start: 0.8119 (tppp) cc_final: 0.7612 (mmmm) REVERT: A 251 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7429 (tm-30) REVERT: A 252 LYS cc_start: 0.8474 (ptpp) cc_final: 0.8203 (ptpp) REVERT: A 258 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8647 (mm-40) REVERT: A 279 MET cc_start: 0.8556 (mtt) cc_final: 0.8150 (mtm) REVERT: B 76 THR cc_start: 0.7846 (p) cc_final: 0.7377 (p) REVERT: B 80 LYS cc_start: 0.9012 (mttt) cc_final: 0.8722 (mttp) REVERT: B 143 LEU cc_start: 0.9279 (mt) cc_final: 0.8966 (mt) REVERT: B 145 MET cc_start: 0.6984 (mpp) cc_final: 0.6544 (mpp) REVERT: B 184 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 190 GLN cc_start: 0.8686 (pt0) cc_final: 0.8354 (pt0) REVERT: B 209 MET cc_start: 0.0216 (tpt) cc_final: -0.0268 (mmm) REVERT: B 232 ASN cc_start: 0.7422 (m-40) cc_final: 0.6416 (p0) REVERT: B 289 ASN cc_start: 0.8692 (p0) cc_final: 0.8386 (p0) REVERT: B 292 TYR cc_start: 0.8661 (m-10) cc_final: 0.8329 (m-10) REVERT: C 112 GLU cc_start: 0.8770 (pt0) cc_final: 0.8401 (pt0) REVERT: C 145 MET cc_start: 0.6689 (mpp) cc_final: 0.6183 (mpp) REVERT: C 184 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 209 MET cc_start: -0.1659 (mmm) cc_final: -0.1960 (mmm) REVERT: C 232 ASN cc_start: 0.7583 (m-40) cc_final: 0.6485 (p0) REVERT: C 233 LYS cc_start: 0.7891 (tppp) cc_final: 0.7364 (mmmm) REVERT: C 258 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8576 (tp40) REVERT: C 271 ASN cc_start: 0.8581 (t0) cc_final: 0.8339 (t0) REVERT: C 279 MET cc_start: 0.8413 (mtm) cc_final: 0.8159 (mmp) REVERT: D 122 MET cc_start: 0.7307 (tmm) cc_final: 0.6979 (tmm) REVERT: D 145 MET cc_start: 0.7174 (mpp) cc_final: 0.6797 (mpp) REVERT: D 184 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8218 (mt-10) REVERT: D 209 MET cc_start: -0.0371 (tpt) cc_final: -0.0799 (mmm) REVERT: D 232 ASN cc_start: 0.7702 (m-40) cc_final: 0.6442 (p0) REVERT: D 235 LYS cc_start: 0.9200 (mttt) cc_final: 0.8807 (mmmt) REVERT: D 251 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7139 (tm-30) REVERT: D 258 GLN cc_start: 0.9129 (tp40) cc_final: 0.8708 (tp40) REVERT: D 271 ASN cc_start: 0.8852 (t0) cc_final: 0.8584 (p0) REVERT: D 298 ARG cc_start: 0.8530 (mpt180) cc_final: 0.7838 (mmt-90) REVERT: E 145 MET cc_start: 0.6708 (mpp) cc_final: 0.5928 (mpp) REVERT: E 232 ASN cc_start: 0.7550 (m-40) cc_final: 0.6181 (p0) REVERT: E 233 LYS cc_start: 0.8315 (tppp) cc_final: 0.7613 (mmmm) REVERT: E 240 LYS cc_start: 0.8538 (mttm) cc_final: 0.8017 (ttpt) REVERT: E 251 GLU cc_start: 0.8497 (mm-30) cc_final: 0.6902 (tm-30) REVERT: E 252 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7615 (tppt) REVERT: E 258 GLN cc_start: 0.9118 (tp40) cc_final: 0.8526 (tp40) REVERT: E 292 TYR cc_start: 0.8331 (m-80) cc_final: 0.8042 (m-80) REVERT: F 143 LEU cc_start: 0.9392 (mt) cc_final: 0.8896 (mt) REVERT: F 162 ARG cc_start: 0.7936 (tmt170) cc_final: 0.7703 (ttt180) REVERT: F 173 ASP cc_start: 0.8372 (t0) cc_final: 0.7177 (m-30) REVERT: F 174 GLU cc_start: 0.8242 (tt0) cc_final: 0.7805 (tm-30) REVERT: F 182 VAL cc_start: 0.8018 (t) cc_final: 0.7693 (t) REVERT: F 209 MET cc_start: 0.2653 (mtt) cc_final: 0.0339 (ttt) REVERT: F 232 ASN cc_start: 0.7594 (m-40) cc_final: 0.6144 (p0) REVERT: F 235 LYS cc_start: 0.9160 (mttt) cc_final: 0.8684 (mmmt) REVERT: F 258 GLN cc_start: 0.8886 (tp40) cc_final: 0.8618 (tp-100) REVERT: G 73 PHE cc_start: 0.7559 (t80) cc_final: 0.6725 (t80) REVERT: G 80 LYS cc_start: 0.8879 (mttt) cc_final: 0.8624 (mttp) REVERT: G 108 GLU cc_start: 0.7855 (tp30) cc_final: 0.7136 (tp30) REVERT: G 145 MET cc_start: 0.6805 (mpp) cc_final: 0.6139 (mpp) REVERT: G 184 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8072 (mt-10) REVERT: G 232 ASN cc_start: 0.7324 (m-40) cc_final: 0.6588 (p0) REVERT: G 233 LYS cc_start: 0.8062 (tppp) cc_final: 0.7702 (mmmm) REVERT: G 251 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7395 (tm-30) REVERT: G 258 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8625 (tp-100) REVERT: H 76 THR cc_start: 0.8500 (p) cc_final: 0.8014 (p) REVERT: H 80 LYS cc_start: 0.8914 (mttt) cc_final: 0.8676 (mttp) REVERT: H 145 MET cc_start: 0.7324 (mpp) cc_final: 0.6815 (mpp) REVERT: H 182 VAL cc_start: 0.8371 (t) cc_final: 0.8154 (t) REVERT: H 209 MET cc_start: 0.2179 (mtt) cc_final: 0.0994 (mtp) REVERT: H 228 ARG cc_start: 0.7088 (tmt-80) cc_final: 0.6686 (tmt170) REVERT: H 236 LYS cc_start: 0.8586 (tptp) cc_final: 0.8366 (tppt) REVERT: H 251 GLU cc_start: 0.8778 (mm-30) cc_final: 0.7530 (tm-30) REVERT: H 252 LYS cc_start: 0.8691 (ptpp) cc_final: 0.7863 (tppt) REVERT: H 271 ASN cc_start: 0.8920 (t0) cc_final: 0.8662 (t0) REVERT: H 291 ASP cc_start: 0.7913 (p0) cc_final: 0.7559 (p0) REVERT: I 76 THR cc_start: 0.7991 (p) cc_final: 0.7699 (p) REVERT: I 80 LYS cc_start: 0.8931 (mttt) cc_final: 0.8697 (mttp) REVERT: I 145 MET cc_start: 0.7394 (mpp) cc_final: 0.6926 (mpp) REVERT: I 190 GLN cc_start: 0.7994 (pp30) cc_final: 0.7790 (pp30) REVERT: I 232 ASN cc_start: 0.7407 (m-40) cc_final: 0.6501 (p0) REVERT: I 233 LYS cc_start: 0.8223 (tppp) cc_final: 0.7894 (mmmm) REVERT: I 251 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7308 (tm-30) REVERT: I 258 GLN cc_start: 0.8824 (tp40) cc_final: 0.8617 (mm-40) REVERT: J 73 PHE cc_start: 0.7744 (t80) cc_final: 0.6822 (t80) REVERT: J 83 TRP cc_start: 0.7969 (m-10) cc_final: 0.7260 (m-10) REVERT: J 86 MET cc_start: 0.7444 (ttm) cc_final: 0.6718 (ttm) REVERT: J 108 GLU cc_start: 0.7591 (tp30) cc_final: 0.6943 (tp30) REVERT: J 112 GLU cc_start: 0.7386 (tp30) cc_final: 0.7181 (tp30) REVERT: J 113 TYR cc_start: 0.8853 (t80) cc_final: 0.8089 (t80) REVERT: J 142 GLU cc_start: 0.8155 (tp30) cc_final: 0.7667 (tp30) REVERT: J 145 MET cc_start: 0.7430 (mpp) cc_final: 0.7041 (mpp) REVERT: J 232 ASN cc_start: 0.7590 (m-40) cc_final: 0.6704 (p0) REVERT: J 233 LYS cc_start: 0.8253 (tppp) cc_final: 0.7852 (mmmm) REVERT: J 251 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7263 (tm-30) REVERT: J 258 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8503 (tp40) REVERT: K 73 PHE cc_start: 0.7687 (t80) cc_final: 0.6688 (t80) REVERT: K 80 LYS cc_start: 0.8793 (mttt) cc_final: 0.8556 (mttp) REVERT: K 108 GLU cc_start: 0.7927 (tp30) cc_final: 0.7156 (tp30) REVERT: K 145 MET cc_start: 0.7290 (mpp) cc_final: 0.6941 (mpp) REVERT: K 235 LYS cc_start: 0.9175 (mttt) cc_final: 0.8688 (mmmt) REVERT: K 236 LYS cc_start: 0.8634 (tptp) cc_final: 0.8401 (tppt) REVERT: K 251 GLU cc_start: 0.8632 (mm-30) cc_final: 0.7378 (tm-30) REVERT: K 279 MET cc_start: 0.8633 (mtm) cc_final: 0.8069 (mmp) REVERT: L 112 GLU cc_start: 0.7297 (tp30) cc_final: 0.7085 (tp30) REVERT: L 145 MET cc_start: 0.7187 (mpp) cc_final: 0.6814 (mpp) REVERT: L 174 GLU cc_start: 0.8589 (pm20) cc_final: 0.7898 (pt0) REVERT: L 177 HIS cc_start: 0.7890 (m170) cc_final: 0.6912 (m90) REVERT: L 232 ASN cc_start: 0.7579 (m-40) cc_final: 0.6456 (p0) REVERT: L 251 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7410 (tm-30) REVERT: L 252 LYS cc_start: 0.8505 (ptpp) cc_final: 0.8052 (tppt) REVERT: L 260 ILE cc_start: 0.9053 (mt) cc_final: 0.8698 (mt) REVERT: L 279 MET cc_start: 0.8491 (mtm) cc_final: 0.8027 (mmp) REVERT: L 295 GLN cc_start: 0.9470 (mt0) cc_final: 0.8971 (mt0) REVERT: L 298 ARG cc_start: 0.8806 (mpt-90) cc_final: 0.8591 (ppt170) REVERT: M 108 GLU cc_start: 0.8222 (tp30) cc_final: 0.7821 (tp30) REVERT: M 112 GLU cc_start: 0.8603 (pt0) cc_final: 0.7703 (pt0) REVERT: M 145 MET cc_start: 0.7037 (mpp) cc_final: 0.6550 (mpp) REVERT: M 184 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8252 (pt0) REVERT: M 200 MET cc_start: 0.7241 (tpp) cc_final: 0.6690 (mmm) REVERT: M 232 ASN cc_start: 0.7499 (m-40) cc_final: 0.6361 (p0) REVERT: M 251 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7515 (tm-30) REVERT: M 258 GLN cc_start: 0.9076 (tp40) cc_final: 0.8572 (tp40) REVERT: N 80 LYS cc_start: 0.8918 (mttt) cc_final: 0.8706 (mttp) REVERT: N 112 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7205 (mt-10) REVERT: N 145 MET cc_start: 0.7492 (mpp) cc_final: 0.6954 (mpp) REVERT: N 184 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8395 (pt0) REVERT: N 205 VAL cc_start: 0.6174 (t) cc_final: 0.5648 (t) REVERT: N 209 MET cc_start: 0.2797 (mtt) cc_final: 0.1618 (mtp) REVERT: N 229 THR cc_start: 0.6230 (p) cc_final: 0.5227 (t) REVERT: N 232 ASN cc_start: 0.7351 (m-40) cc_final: 0.6757 (p0) REVERT: N 251 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7492 (tm-30) REVERT: N 258 GLN cc_start: 0.9023 (tp40) cc_final: 0.8598 (tp-100) REVERT: O 145 MET cc_start: 0.7268 (mpp) cc_final: 0.7017 (mpp) REVERT: O 184 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8373 (mt-10) REVERT: O 251 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7260 (tm-30) REVERT: O 258 GLN cc_start: 0.8985 (tp40) cc_final: 0.8521 (mm-40) REVERT: O 259 GLN cc_start: 0.9288 (tp40) cc_final: 0.9035 (tp40) REVERT: O 298 ARG cc_start: 0.8806 (mpt-90) cc_final: 0.8365 (mmt-90) REVERT: P 101 ASN cc_start: 0.7526 (m110) cc_final: 0.7301 (m-40) REVERT: P 121 TRP cc_start: 0.8568 (m-90) cc_final: 0.8248 (m-90) REVERT: P 143 LEU cc_start: 0.9313 (mt) cc_final: 0.8678 (mm) REVERT: P 145 MET cc_start: 0.6840 (mpp) cc_final: 0.6210 (mpp) REVERT: P 232 ASN cc_start: 0.7354 (m-40) cc_final: 0.6362 (p0) REVERT: P 235 LYS cc_start: 0.9073 (mttt) cc_final: 0.8722 (mmmt) REVERT: P 251 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7538 (tm-30) REVERT: P 252 LYS cc_start: 0.8713 (ptpp) cc_final: 0.7852 (tppt) REVERT: P 258 GLN cc_start: 0.9023 (tp40) cc_final: 0.8529 (tp40) REVERT: P 271 ASN cc_start: 0.9176 (t0) cc_final: 0.8898 (p0) REVERT: P 279 MET cc_start: 0.8298 (mtm) cc_final: 0.7782 (mmp) REVERT: Q 108 GLU cc_start: 0.8216 (tp30) cc_final: 0.7842 (tp30) REVERT: Q 112 GLU cc_start: 0.8644 (pt0) cc_final: 0.7924 (pt0) REVERT: Q 142 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7407 (tp30) REVERT: Q 143 LEU cc_start: 0.9271 (mt) cc_final: 0.8285 (mm) REVERT: Q 145 MET cc_start: 0.6685 (mpp) cc_final: 0.5780 (mpp) REVERT: Q 162 ARG cc_start: 0.7367 (ttt180) cc_final: 0.7136 (ttt180) REVERT: Q 182 VAL cc_start: 0.8363 (t) cc_final: 0.8145 (t) REVERT: Q 190 GLN cc_start: 0.8417 (pt0) cc_final: 0.8170 (pt0) REVERT: Q 209 MET cc_start: -0.0070 (ttt) cc_final: -0.0982 (mmm) REVERT: Q 228 ARG cc_start: 0.7736 (ttp80) cc_final: 0.6116 (tmt170) REVERT: Q 232 ASN cc_start: 0.7335 (m-40) cc_final: 0.6504 (p0) REVERT: Q 240 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8459 (tttm) REVERT: Q 251 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7422 (tm-30) REVERT: Q 252 LYS cc_start: 0.8501 (ptpp) cc_final: 0.7447 (tppt) REVERT: R 86 MET cc_start: 0.6983 (tpp) cc_final: 0.6252 (ttm) REVERT: R 121 TRP cc_start: 0.8469 (m-90) cc_final: 0.8195 (m-90) REVERT: R 143 LEU cc_start: 0.9284 (mt) cc_final: 0.8999 (mm) REVERT: R 145 MET cc_start: 0.6909 (mpp) cc_final: 0.6598 (mpp) REVERT: R 232 ASN cc_start: 0.7239 (m-40) cc_final: 0.6768 (p0) REVERT: R 251 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7503 (tm-30) REVERT: R 258 GLN cc_start: 0.8887 (tp40) cc_final: 0.8409 (mm-40) REVERT: R 279 MET cc_start: 0.8521 (mtm) cc_final: 0.7925 (mmp) REVERT: R 289 ASN cc_start: 0.8792 (p0) cc_final: 0.8387 (p0) REVERT: R 292 TYR cc_start: 0.8719 (m-10) cc_final: 0.8465 (m-10) outliers start: 2 outliers final: 0 residues processed: 1169 average time/residue: 0.2295 time to fit residues: 417.0773 Evaluate side-chains 1033 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1033 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 409 optimal weight: 0.9980 chunk 377 optimal weight: 0.0670 chunk 110 optimal weight: 7.9990 chunk 159 optimal weight: 30.0000 chunk 313 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 291 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS C 295 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN G 167 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 ASN ** L 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 146 ASN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN N 146 ASN ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.175645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139636 restraints weight = 64722.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144595 restraints weight = 43888.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.148212 restraints weight = 32493.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150888 restraints weight = 25720.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152897 restraints weight = 21414.188| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.7811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34326 Z= 0.141 Angle : 0.764 14.867 46422 Z= 0.369 Chirality : 0.045 0.256 5346 Planarity : 0.004 0.084 5940 Dihedral : 9.867 146.964 4842 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4158 helix: 0.87 (0.10), residues: 2574 sheet: -1.11 (0.21), residues: 594 loop : 0.31 (0.22), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 194 TYR 0.015 0.001 TYR J 113 PHE 0.027 0.001 PHE N 297 TRP 0.024 0.001 TRP G 246 HIS 0.008 0.001 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00307 (34326) covalent geometry : angle 0.76391 (46422) hydrogen bonds : bond 0.03218 ( 1852) hydrogen bonds : angle 4.27280 ( 5448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1149 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 THR cc_start: 0.8245 (p) cc_final: 0.7832 (p) REVERT: A 80 LYS cc_start: 0.8862 (mttt) cc_final: 0.8625 (mttp) REVERT: A 143 LEU cc_start: 0.9417 (mt) cc_final: 0.9034 (mt) REVERT: A 145 MET cc_start: 0.7408 (mpp) cc_final: 0.6856 (mpp) REVERT: A 169 LEU cc_start: 0.8360 (tp) cc_final: 0.8067 (tp) REVERT: A 228 ARG cc_start: 0.6965 (tmt-80) cc_final: 0.6760 (tmt170) REVERT: A 232 ASN cc_start: 0.7544 (m-40) cc_final: 0.6392 (p0) REVERT: A 233 LYS cc_start: 0.8138 (tppp) cc_final: 0.7765 (mmmm) REVERT: A 235 LYS cc_start: 0.8933 (mttt) cc_final: 0.8608 (ptpp) REVERT: A 251 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7420 (tm-30) REVERT: A 252 LYS cc_start: 0.8453 (ptpp) cc_final: 0.8181 (ptpp) REVERT: A 258 GLN cc_start: 0.8846 (tp-100) cc_final: 0.8580 (mm-40) REVERT: A 279 MET cc_start: 0.8543 (mtt) cc_final: 0.8156 (mtm) REVERT: B 76 THR cc_start: 0.7752 (p) cc_final: 0.7316 (p) REVERT: B 80 LYS cc_start: 0.8983 (mttt) cc_final: 0.8701 (mttp) REVERT: B 122 MET cc_start: 0.8174 (ptm) cc_final: 0.7582 (ppp) REVERT: B 123 ILE cc_start: 0.9417 (pt) cc_final: 0.8920 (pt) REVERT: B 143 LEU cc_start: 0.9223 (mt) cc_final: 0.8956 (mt) REVERT: B 145 MET cc_start: 0.6940 (mpp) cc_final: 0.6556 (mpp) REVERT: B 184 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 190 GLN cc_start: 0.8603 (pt0) cc_final: 0.8278 (pt0) REVERT: B 209 MET cc_start: 0.0086 (tpt) cc_final: -0.0294 (mmm) REVERT: B 235 LYS cc_start: 0.8991 (mttt) cc_final: 0.8479 (mmmt) REVERT: B 270 LEU cc_start: 0.9317 (tt) cc_final: 0.9002 (tp) REVERT: B 289 ASN cc_start: 0.8675 (p0) cc_final: 0.8007 (p0) REVERT: B 291 ASP cc_start: 0.8974 (t0) cc_final: 0.8697 (p0) REVERT: C 112 GLU cc_start: 0.8677 (pt0) cc_final: 0.8405 (pt0) REVERT: C 145 MET cc_start: 0.6542 (mpp) cc_final: 0.6178 (mpp) REVERT: C 209 MET cc_start: -0.1642 (mmm) cc_final: -0.1959 (mmm) REVERT: C 233 LYS cc_start: 0.7916 (tppp) cc_final: 0.7710 (mmmm) REVERT: C 258 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8792 (mm-40) REVERT: C 275 ARG cc_start: 0.8012 (ptp90) cc_final: 0.7702 (ptp90) REVERT: C 279 MET cc_start: 0.8340 (mtm) cc_final: 0.8083 (mmp) REVERT: D 122 MET cc_start: 0.7368 (tmm) cc_final: 0.7047 (tmm) REVERT: D 145 MET cc_start: 0.7098 (mpp) cc_final: 0.6779 (mpp) REVERT: D 209 MET cc_start: -0.0601 (tpt) cc_final: -0.1020 (mmm) REVERT: D 232 ASN cc_start: 0.7671 (m-40) cc_final: 0.6367 (p0) REVERT: D 235 LYS cc_start: 0.9176 (mttt) cc_final: 0.8807 (mmmt) REVERT: D 251 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7098 (tm-30) REVERT: D 258 GLN cc_start: 0.9089 (tp40) cc_final: 0.8677 (tp40) REVERT: D 271 ASN cc_start: 0.8744 (t0) cc_final: 0.8087 (t0) REVERT: D 279 MET cc_start: 0.8482 (mtm) cc_final: 0.7912 (mmp) REVERT: D 298 ARG cc_start: 0.8490 (mpt180) cc_final: 0.7783 (mmt-90) REVERT: E 145 MET cc_start: 0.6753 (mpp) cc_final: 0.6071 (mpp) REVERT: E 232 ASN cc_start: 0.7533 (m-40) cc_final: 0.6190 (p0) REVERT: E 233 LYS cc_start: 0.8359 (tppp) cc_final: 0.7695 (mmmm) REVERT: E 240 LYS cc_start: 0.8536 (mttm) cc_final: 0.8007 (ttpt) REVERT: E 251 GLU cc_start: 0.8456 (mm-30) cc_final: 0.6899 (tm-30) REVERT: E 252 LYS cc_start: 0.8424 (ptpp) cc_final: 0.7587 (tppt) REVERT: E 258 GLN cc_start: 0.9090 (tp40) cc_final: 0.8536 (tp40) REVERT: F 143 LEU cc_start: 0.9398 (mt) cc_final: 0.9118 (mt) REVERT: F 173 ASP cc_start: 0.8290 (t0) cc_final: 0.7172 (m-30) REVERT: F 174 GLU cc_start: 0.8191 (tt0) cc_final: 0.7898 (tm-30) REVERT: F 209 MET cc_start: 0.2742 (mtt) cc_final: 0.0430 (ttt) REVERT: F 232 ASN cc_start: 0.7539 (m-40) cc_final: 0.6057 (p0) REVERT: F 258 GLN cc_start: 0.8895 (tp40) cc_final: 0.8577 (tp-100) REVERT: G 73 PHE cc_start: 0.7495 (t80) cc_final: 0.6643 (t80) REVERT: G 108 GLU cc_start: 0.7612 (tp30) cc_final: 0.6986 (tp30) REVERT: G 142 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7437 (tp30) REVERT: G 145 MET cc_start: 0.7057 (mpp) cc_final: 0.6353 (mpp) REVERT: G 184 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7978 (mt-10) REVERT: G 232 ASN cc_start: 0.7375 (m-40) cc_final: 0.6646 (p0) REVERT: G 233 LYS cc_start: 0.8121 (tppp) cc_final: 0.7752 (mmmm) REVERT: G 251 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7373 (tm-30) REVERT: H 76 THR cc_start: 0.8344 (p) cc_final: 0.7894 (p) REVERT: H 80 LYS cc_start: 0.8905 (mttt) cc_final: 0.8678 (mttp) REVERT: H 145 MET cc_start: 0.7284 (mpp) cc_final: 0.6747 (mpp) REVERT: H 182 VAL cc_start: 0.8270 (t) cc_final: 0.8024 (t) REVERT: H 209 MET cc_start: 0.2219 (mtt) cc_final: 0.1058 (mtp) REVERT: H 251 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7531 (tm-30) REVERT: H 252 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8317 (ptpp) REVERT: H 270 LEU cc_start: 0.9290 (tt) cc_final: 0.8930 (pp) REVERT: H 271 ASN cc_start: 0.8790 (t0) cc_final: 0.8530 (t0) REVERT: H 291 ASP cc_start: 0.7951 (p0) cc_final: 0.7543 (p0) REVERT: I 76 THR cc_start: 0.7898 (p) cc_final: 0.7563 (p) REVERT: I 80 LYS cc_start: 0.8942 (mttt) cc_final: 0.8687 (mttp) REVERT: I 145 MET cc_start: 0.7358 (mpp) cc_final: 0.6899 (mpp) REVERT: I 190 GLN cc_start: 0.7877 (pp30) cc_final: 0.7650 (pp30) REVERT: I 232 ASN cc_start: 0.7335 (m-40) cc_final: 0.6510 (p0) REVERT: I 233 LYS cc_start: 0.8253 (tppp) cc_final: 0.7885 (mmmm) REVERT: I 251 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7297 (tm-30) REVERT: I 258 GLN cc_start: 0.8826 (tp40) cc_final: 0.8585 (mm-40) REVERT: I 292 TYR cc_start: 0.8770 (m-10) cc_final: 0.8258 (m-80) REVERT: J 73 PHE cc_start: 0.7634 (t80) cc_final: 0.6787 (t80) REVERT: J 83 TRP cc_start: 0.7973 (m-10) cc_final: 0.7383 (m-10) REVERT: J 108 GLU cc_start: 0.7469 (tp30) cc_final: 0.6881 (tp30) REVERT: J 142 GLU cc_start: 0.7989 (tp30) cc_final: 0.7403 (tp30) REVERT: J 145 MET cc_start: 0.7156 (mpp) cc_final: 0.6362 (mpp) REVERT: J 174 GLU cc_start: 0.7999 (tp30) cc_final: 0.7395 (tp30) REVERT: J 232 ASN cc_start: 0.7534 (m-40) cc_final: 0.6606 (p0) REVERT: J 233 LYS cc_start: 0.8218 (tppp) cc_final: 0.7860 (mmmm) REVERT: J 251 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7228 (tm-30) REVERT: J 258 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8447 (tp40) REVERT: K 73 PHE cc_start: 0.7646 (t80) cc_final: 0.6731 (t80) REVERT: K 76 THR cc_start: 0.8016 (p) cc_final: 0.7291 (p) REVERT: K 80 LYS cc_start: 0.8792 (mttt) cc_final: 0.8537 (mttp) REVERT: K 108 GLU cc_start: 0.7835 (tp30) cc_final: 0.7086 (tp30) REVERT: K 145 MET cc_start: 0.7300 (mpp) cc_final: 0.6902 (mpp) REVERT: K 232 ASN cc_start: 0.7392 (m-40) cc_final: 0.6510 (p0) REVERT: K 235 LYS cc_start: 0.9119 (mttt) cc_final: 0.8677 (mmmt) REVERT: K 251 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7376 (tm-30) REVERT: K 279 MET cc_start: 0.8606 (mtm) cc_final: 0.8033 (mmp) REVERT: K 294 ARG cc_start: 0.9031 (mmt90) cc_final: 0.8195 (mmm160) REVERT: K 298 ARG cc_start: 0.8792 (mpt180) cc_final: 0.8039 (mmt-90) REVERT: L 145 MET cc_start: 0.6769 (mpp) cc_final: 0.6078 (mmt) REVERT: L 174 GLU cc_start: 0.8430 (pm20) cc_final: 0.7700 (tt0) REVERT: L 177 HIS cc_start: 0.7770 (m170) cc_final: 0.6690 (m90) REVERT: L 232 ASN cc_start: 0.7635 (m-40) cc_final: 0.6438 (p0) REVERT: L 251 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7410 (tm-30) REVERT: L 279 MET cc_start: 0.8528 (mtm) cc_final: 0.8031 (mmp) REVERT: L 295 GLN cc_start: 0.9440 (mt0) cc_final: 0.8967 (mt0) REVERT: L 298 ARG cc_start: 0.8782 (mpt-90) cc_final: 0.8571 (ppt170) REVERT: M 108 GLU cc_start: 0.8045 (tp30) cc_final: 0.7794 (tp30) REVERT: M 112 GLU cc_start: 0.8547 (pt0) cc_final: 0.7582 (pt0) REVERT: M 121 TRP cc_start: 0.8555 (m-90) cc_final: 0.8350 (m-90) REVERT: M 145 MET cc_start: 0.6493 (mpp) cc_final: 0.5795 (mmt) REVERT: M 200 MET cc_start: 0.7287 (tpp) cc_final: 0.6776 (mmm) REVERT: M 232 ASN cc_start: 0.7515 (m-40) cc_final: 0.6324 (p0) REVERT: M 251 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7481 (tm-30) REVERT: M 258 GLN cc_start: 0.9077 (tp40) cc_final: 0.8666 (tp40) REVERT: N 112 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7103 (mt-10) REVERT: N 145 MET cc_start: 0.7407 (mpp) cc_final: 0.6914 (mpp) REVERT: N 205 VAL cc_start: 0.6170 (t) cc_final: 0.5654 (t) REVERT: N 209 MET cc_start: 0.2722 (mtt) cc_final: 0.0705 (ttt) REVERT: N 229 THR cc_start: 0.6241 (p) cc_final: 0.5177 (t) REVERT: N 232 ASN cc_start: 0.7398 (m-40) cc_final: 0.6847 (p0) REVERT: N 251 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7409 (tm-30) REVERT: N 258 GLN cc_start: 0.8964 (tp40) cc_final: 0.8553 (tp-100) REVERT: O 112 GLU cc_start: 0.8568 (pt0) cc_final: 0.7834 (pt0) REVERT: O 145 MET cc_start: 0.7127 (mpp) cc_final: 0.6878 (mpp) REVERT: O 184 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8307 (mt-10) REVERT: O 251 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7261 (tm-30) REVERT: O 258 GLN cc_start: 0.8981 (tp40) cc_final: 0.8599 (tp-100) REVERT: O 298 ARG cc_start: 0.8794 (mpt-90) cc_final: 0.8336 (mmt-90) REVERT: P 81 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8553 (pp30) REVERT: P 101 ASN cc_start: 0.7448 (m110) cc_final: 0.7163 (m-40) REVERT: P 112 GLU cc_start: 0.8725 (pt0) cc_final: 0.7662 (pt0) REVERT: P 182 VAL cc_start: 0.8219 (t) cc_final: 0.8015 (t) REVERT: P 232 ASN cc_start: 0.7299 (m-40) cc_final: 0.6219 (p0) REVERT: P 235 LYS cc_start: 0.9050 (mttt) cc_final: 0.8732 (mmmt) REVERT: P 251 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7551 (tm-30) REVERT: P 252 LYS cc_start: 0.8697 (ptpp) cc_final: 0.7836 (tppt) REVERT: P 258 GLN cc_start: 0.8986 (tp40) cc_final: 0.8490 (tp40) REVERT: P 271 ASN cc_start: 0.9105 (t0) cc_final: 0.8778 (p0) REVERT: P 279 MET cc_start: 0.8153 (mtm) cc_final: 0.7747 (mmp) REVERT: Q 108 GLU cc_start: 0.8029 (tp30) cc_final: 0.7735 (tp30) REVERT: Q 112 GLU cc_start: 0.8575 (pt0) cc_final: 0.7752 (pt0) REVERT: Q 142 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7352 (tp30) REVERT: Q 143 LEU cc_start: 0.9312 (mt) cc_final: 0.8296 (mm) REVERT: Q 145 MET cc_start: 0.6588 (mpp) cc_final: 0.5742 (mpp) REVERT: Q 182 VAL cc_start: 0.8357 (t) cc_final: 0.8097 (t) REVERT: Q 190 GLN cc_start: 0.8373 (pt0) cc_final: 0.8108 (pt0) REVERT: Q 209 MET cc_start: -0.0090 (ttt) cc_final: -0.0987 (mmm) REVERT: Q 228 ARG cc_start: 0.7820 (ttp80) cc_final: 0.6552 (tpt90) REVERT: Q 232 ASN cc_start: 0.7287 (m-40) cc_final: 0.6562 (p0) REVERT: Q 251 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7531 (tm-30) REVERT: Q 252 LYS cc_start: 0.8528 (ptpp) cc_final: 0.7464 (tppt) REVERT: R 86 MET cc_start: 0.7057 (tpp) cc_final: 0.6477 (ttm) REVERT: R 143 LEU cc_start: 0.9250 (mt) cc_final: 0.9044 (mm) REVERT: R 145 MET cc_start: 0.6927 (mpp) cc_final: 0.6585 (mpp) REVERT: R 184 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8056 (pt0) REVERT: R 232 ASN cc_start: 0.7188 (m-40) cc_final: 0.6889 (p0) REVERT: R 251 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7500 (tm-30) REVERT: R 258 GLN cc_start: 0.8838 (tp40) cc_final: 0.8424 (mm-40) REVERT: R 259 GLN cc_start: 0.9124 (tp40) cc_final: 0.8589 (tp40) REVERT: R 279 MET cc_start: 0.8443 (mtm) cc_final: 0.7951 (mmp) REVERT: R 289 ASN cc_start: 0.8799 (p0) cc_final: 0.8376 (p0) REVERT: R 292 TYR cc_start: 0.8650 (m-10) cc_final: 0.8413 (m-10) outliers start: 2 outliers final: 0 residues processed: 1151 average time/residue: 0.2379 time to fit residues: 427.4293 Evaluate side-chains 1014 residues out of total 3564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1014 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 352 optimal weight: 4.9990 chunk 410 optimal weight: 0.1980 chunk 37 optimal weight: 9.9990 chunk 272 optimal weight: 0.0970 chunk 382 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 367 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS C 295 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN G 167 GLN G 258 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 GLN J 272 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN ** K 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 ASN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** M 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 GLN ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 167 GLN ** Q 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 262 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.171184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135109 restraints weight = 64892.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139948 restraints weight = 42977.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143493 restraints weight = 31635.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146109 restraints weight = 25054.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148054 restraints weight = 20900.680| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34326 Z= 0.182 Angle : 0.800 10.646 46422 Z= 0.387 Chirality : 0.046 0.255 5346 Planarity : 0.005 0.083 5940 Dihedral : 10.210 139.735 4842 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.11 % Allowed : 0.70 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 4158 helix: 0.63 (0.10), residues: 2574 sheet: -1.45 (0.20), residues: 630 loop : 0.09 (0.23), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 275 TYR 0.019 0.001 TYR J 113 PHE 0.024 0.002 PHE A 297 TRP 0.030 0.002 TRP K 246 HIS 0.011 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00396 (34326) covalent geometry : angle 0.80028 (46422) hydrogen bonds : bond 0.03339 ( 1852) hydrogen bonds : angle 4.48318 ( 5448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8603.07 seconds wall clock time: 148 minutes 18.49 seconds (8898.49 seconds total)