Starting phenix.real_space_refine on Mon Aug 25 22:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxq_43629/08_2025/8vxq_43629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxq_43629/08_2025/8vxq_43629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vxq_43629/08_2025/8vxq_43629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxq_43629/08_2025/8vxq_43629.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxq_43629/08_2025/8vxq_43629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxq_43629/08_2025/8vxq_43629.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.158 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: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 18963 2.51 5 N 5967 2.21 5 O 6480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31572 Number of models: 1 Model: "" Number of chains: 18 Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "J" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "K" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "L" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "M" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "N" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "O" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "P" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "Q" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "A" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "B" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "C" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "D" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "G" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "H" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "I" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Time building chain proxies: 6.81, per 1000 atoms: 0.22 Number of scatterers: 31572 At special positions: 0 Unit cell: (130.68, 135.52, 309.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 162 16.00 O 6480 8.00 N 5967 7.00 C 18963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7596 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 9 sheets defined 71.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'R' and resid 28 through 68 removed outlier: 3.613A pdb=" N ILE R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL R 66 " --> pdb=" O TYR R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 76 Processing helix chain 'R' and resid 78 through 88 removed outlier: 3.522A pdb=" N GLY R 82 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG R 87 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 141 removed outlier: 5.279A pdb=" N GLY R 131 " --> pdb=" O VAL R 127 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 133 " --> pdb=" O GLN R 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 141 " --> pdb=" O ARG R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.712A pdb=" N GLU R 154 " --> pdb=" O GLN R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 259 removed outlier: 3.671A pdb=" N GLU R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA R 189 " --> pdb=" O GLN R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 291 removed outlier: 4.271A pdb=" N ASN R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 305 removed outlier: 3.509A pdb=" N ARG R 299 " --> pdb=" O SER R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 331 removed outlier: 3.835A pdb=" N ILE R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA R 318 " --> pdb=" O SER R 314 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN R 319 " --> pdb=" O LYS R 315 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN R 322 " --> pdb=" O ALA R 318 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU R 323 " --> pdb=" O GLN R 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU R 331 " --> pdb=" O ARG R 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 68 removed outlier: 4.187A pdb=" N ILE J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 66 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 78 through 90 removed outlier: 3.532A pdb=" N GLY J 82 " --> pdb=" O ASP J 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 141 removed outlier: 3.570A pdb=" N LYS J 105 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 155 removed outlier: 5.438A pdb=" N ALA J 153 " --> pdb=" O ASN J 149 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU J 154 " --> pdb=" O GLN J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 259 removed outlier: 3.814A pdb=" N THR J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE J 174 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN J 175 " --> pdb=" O GLN J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 removed outlier: 4.290A pdb=" N ASN J 286 " --> pdb=" O SER J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 305 Processing helix chain 'J' and resid 316 through 331 removed outlier: 4.579A pdb=" N GLN J 322 " --> pdb=" O ALA J 318 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU J 323 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU J 331 " --> pdb=" O ARG J 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 68 removed outlier: 4.307A pdb=" N ILE K 39 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL K 66 " --> pdb=" O TYR K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 78 through 90 removed outlier: 3.513A pdb=" N GLY K 82 " --> pdb=" O ASP K 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG K 87 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 141 removed outlier: 5.242A pdb=" N GLY K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 141 " --> pdb=" O ARG K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 155 removed outlier: 3.717A pdb=" N ILE K 151 " --> pdb=" O GLU K 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU K 154 " --> pdb=" O GLN K 150 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 259 removed outlier: 4.265A pdb=" N THR K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 removed outlier: 4.230A pdb=" N ASN K 286 " --> pdb=" O SER K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 305 Processing helix chain 'K' and resid 313 through 331 removed outlier: 4.106A pdb=" N ILE K 317 " --> pdb=" O SER K 313 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA K 318 " --> pdb=" O SER K 314 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN K 322 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU K 331 " --> pdb=" O ARG K 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 68 removed outlier: 4.271A pdb=" N ILE L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN L 65 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL L 66 " --> pdb=" O TYR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 76 Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.616A pdb=" N GLY L 82 " --> pdb=" O ASP L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 141 removed outlier: 3.838A pdb=" N LYS L 105 " --> pdb=" O ASP L 101 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY L 131 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE L 132 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 133 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 155 removed outlier: 3.598A pdb=" N ILE L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA L 153 " --> pdb=" O ASN L 149 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU L 154 " --> pdb=" O GLN L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 259 removed outlier: 3.656A pdb=" N GLU L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 287 removed outlier: 4.365A pdb=" N ASN L 286 " --> pdb=" O SER L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 305 Processing helix chain 'L' and resid 316 through 331 removed outlier: 4.128A pdb=" N GLN L 322 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU L 323 " --> pdb=" O GLN L 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU L 331 " --> pdb=" O ARG L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 68 removed outlier: 3.668A pdb=" N ILE M 39 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL M 66 " --> pdb=" O TYR M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 76 Processing helix chain 'M' and resid 78 through 90 removed outlier: 3.503A pdb=" N GLY M 82 " --> pdb=" O ASP M 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN M 86 " --> pdb=" O GLY M 82 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG M 87 " --> pdb=" O LEU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 129 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 145 through 155 removed outlier: 4.157A pdb=" N ASN M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 259 removed outlier: 3.725A pdb=" N GLU M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU M 196 " --> pdb=" O ASN M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 287 removed outlier: 4.288A pdb=" N ASN M 286 " --> pdb=" O SER M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 305 Processing helix chain 'M' and resid 316 through 331 removed outlier: 4.213A pdb=" N GLN M 322 " --> pdb=" O ALA M 318 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU M 323 " --> pdb=" O GLN M 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 68 removed outlier: 4.394A pdb=" N GLN N 31 " --> pdb=" O THR N 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE N 39 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN N 65 " --> pdb=" O SER N 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL N 66 " --> pdb=" O TYR N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 76 Processing helix chain 'N' and resid 78 through 86 removed outlier: 3.638A pdb=" N GLN N 86 " --> pdb=" O GLY N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 141 removed outlier: 5.232A pdb=" N GLY N 131 " --> pdb=" O VAL N 127 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE N 132 " --> pdb=" O GLY N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 259 removed outlier: 4.007A pdb=" N GLU N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU N 167 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 291 removed outlier: 4.320A pdb=" N ASN N 286 " --> pdb=" O SER N 282 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 305 Processing helix chain 'N' and resid 316 through 331 removed outlier: 4.306A pdb=" N GLN N 322 " --> pdb=" O ALA N 318 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU N 323 " --> pdb=" O GLN N 319 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU N 331 " --> pdb=" O ARG N 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 68 removed outlier: 4.265A pdb=" N ILE O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 76 Processing helix chain 'O' and resid 78 through 90 removed outlier: 3.563A pdb=" N GLY O 82 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET O 90 " --> pdb=" O GLN O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 141 removed outlier: 3.692A pdb=" N LYS O 105 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY O 131 " --> pdb=" O VAL O 127 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE O 132 " --> pdb=" O GLY O 128 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP O 134 " --> pdb=" O ARG O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 259 removed outlier: 3.637A pdb=" N LEU O 167 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR O 168 " --> pdb=" O ARG O 164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA O 189 " --> pdb=" O GLN O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 291 removed outlier: 4.088A pdb=" N ASN O 286 " --> pdb=" O SER O 282 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA O 288 " --> pdb=" O ALA O 284 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY O 289 " --> pdb=" O LEU O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 305 removed outlier: 3.501A pdb=" N ARG O 299 " --> pdb=" O SER O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 331 removed outlier: 4.370A pdb=" N GLN O 322 " --> pdb=" O ALA O 318 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU O 323 " --> pdb=" O GLN O 319 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU O 331 " --> pdb=" O ARG O 327 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 68 removed outlier: 3.606A pdb=" N ILE P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL P 66 " --> pdb=" O TYR P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 Processing helix chain 'P' and resid 78 through 86 removed outlier: 3.534A pdb=" N GLY P 82 " --> pdb=" O ASP P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 141 removed outlier: 5.239A pdb=" N GLY P 131 " --> pdb=" O VAL P 127 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE P 132 " --> pdb=" O GLY P 128 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP P 134 " --> pdb=" O ARG P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 150 removed outlier: 3.844A pdb=" N ASN P 149 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN P 150 " --> pdb=" O GLY P 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 145 through 150' Processing helix chain 'P' and resid 150 through 155 removed outlier: 3.545A pdb=" N GLU P 154 " --> pdb=" O GLN P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 259 removed outlier: 4.084A pdb=" N GLU P 166 " --> pdb=" O GLU P 162 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR P 168 " --> pdb=" O ARG P 164 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA P 189 " --> pdb=" O GLN P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 291 removed outlier: 4.280A pdb=" N ASN P 286 " --> pdb=" O SER P 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY P 289 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 305 Processing helix chain 'P' and resid 316 through 331 removed outlier: 4.510A pdb=" N GLN P 322 " --> pdb=" O ALA P 318 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU P 331 " --> pdb=" O ARG P 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 68 removed outlier: 3.915A pdb=" N ILE Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER Q 41 " --> pdb=" O GLY Q 37 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN Q 65 " --> pdb=" O SER Q 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL Q 66 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 76 Processing helix chain 'Q' and resid 78 through 87 removed outlier: 3.624A pdb=" N GLY Q 82 " --> pdb=" O ASP Q 78 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 141 removed outlier: 3.687A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY Q 131 " --> pdb=" O VAL Q 127 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE Q 132 " --> pdb=" O GLY Q 128 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 155 removed outlier: 3.833A pdb=" N GLU Q 154 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 259 removed outlier: 4.001A pdb=" N GLU Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 291 removed outlier: 4.279A pdb=" N ASN Q 286 " --> pdb=" O SER Q 282 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA Q 288 " --> pdb=" O ALA Q 284 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY Q 289 " --> pdb=" O LEU Q 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 305 removed outlier: 3.500A pdb=" N ARG Q 299 " --> pdb=" O SER Q 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 316 through 331 removed outlier: 4.198A pdb=" N GLN Q 322 " --> pdb=" O ALA Q 318 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU Q 323 " --> pdb=" O GLN Q 319 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Q 331 " --> pdb=" O ARG Q 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.933A pdb=" N MET A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 138 removed outlier: 3.725A pdb=" N ALA A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.760A pdb=" N MET B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 138 removed outlier: 3.919A pdb=" N ALA B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'C' and resid 6 through 15 removed outlier: 4.075A pdb=" N PHE C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.594A pdb=" N MET C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 138 removed outlier: 3.975A pdb=" N ALA C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.616A pdb=" N TYR C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.212A pdb=" N PHE D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.589A pdb=" N SER D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.701A pdb=" N MET D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 138 removed outlier: 3.841A pdb=" N ALA D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'E' and resid 6 through 15 removed outlier: 4.343A pdb=" N PHE E 10 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 15 " --> pdb=" O GLY E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 65 removed outlier: 3.834A pdb=" N MET E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 138 removed outlier: 3.901A pdb=" N ALA E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 152 removed outlier: 3.751A pdb=" N TYR E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 59 through 65 removed outlier: 3.932A pdb=" N MET F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 138 removed outlier: 3.973A pdb=" N ALA F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 152 removed outlier: 3.558A pdb=" N TYR F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 15 removed outlier: 3.800A pdb=" N GLY G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 65 removed outlier: 4.386A pdb=" N MET G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 138 removed outlier: 3.617A pdb=" N ALA G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'H' and resid 6 through 15 removed outlier: 4.037A pdb=" N PHE H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 49 Processing helix chain 'H' and resid 51 through 56 removed outlier: 4.538A pdb=" N ASN H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 65 removed outlier: 3.658A pdb=" N MET H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 138 removed outlier: 4.098A pdb=" N ALA H 133 " --> pdb=" O ASP H 129 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.934A pdb=" N TYR H 148 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.051A pdb=" N PHE I 10 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'I' and resid 77 through 138 removed outlier: 4.310A pdb=" N ALA I 133 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG I 134 " --> pdb=" O ARG I 130 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 152 removed outlier: 3.656A pdb=" N TYR I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AA7, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'I' and resid 66 through 67 2290 hydrogen bonds defined for protein. 6843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5917 1.32 - 1.44: 7681 1.44 - 1.57: 17938 1.57 - 1.69: 0 1.69 - 1.82: 324 Bond restraints: 31860 Sorted by residual: bond pdb=" CA SER I 59 " pdb=" CB SER I 59 " ideal model delta sigma weight residual 1.532 1.457 0.075 1.58e-02 4.01e+03 2.26e+01 bond pdb=" C ALA K 210 " pdb=" N PHE K 211 " ideal model delta sigma weight residual 1.334 1.277 0.058 1.33e-02 5.65e+03 1.89e+01 bond pdb=" C GLN Q 215 " pdb=" N ARG Q 216 " ideal model delta sigma weight residual 1.334 1.278 0.057 1.33e-02 5.65e+03 1.82e+01 bond pdb=" C PHE K 211 " pdb=" O PHE K 211 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.16e-02 7.43e+03 1.53e+01 bond pdb=" C ARG K 216 " pdb=" N ASP K 217 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.40e-02 5.10e+03 1.18e+01 ... (remaining 31855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 42052 2.29 - 4.58: 722 4.58 - 6.87: 71 6.87 - 9.17: 18 9.17 - 11.46: 4 Bond angle restraints: 42867 Sorted by residual: angle pdb=" C GLN Q 215 " pdb=" N ARG Q 216 " pdb=" CA ARG Q 216 " ideal model delta sigma weight residual 120.44 109.67 10.77 1.36e+00 5.41e-01 6.27e+01 angle pdb=" C ARG K 216 " pdb=" CA ARG K 216 " pdb=" CB ARG K 216 " ideal model delta sigma weight residual 110.95 99.74 11.21 1.55e+00 4.16e-01 5.23e+01 angle pdb=" CA PHE P 211 " pdb=" CB PHE P 211 " pdb=" CG PHE P 211 " ideal model delta sigma weight residual 113.80 119.91 -6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C ALA K 210 " pdb=" N PHE K 211 " pdb=" CA PHE K 211 " ideal model delta sigma weight residual 120.44 112.64 7.80 1.36e+00 5.41e-01 3.29e+01 angle pdb=" C PHE P 211 " pdb=" N THR P 212 " pdb=" CA THR P 212 " ideal model delta sigma weight residual 120.38 112.27 8.11 1.46e+00 4.69e-01 3.09e+01 ... (remaining 42862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16422 17.97 - 35.93: 2412 35.93 - 53.90: 721 53.90 - 71.87: 145 71.87 - 89.83: 46 Dihedral angle restraints: 19746 sinusoidal: 7929 harmonic: 11817 Sorted by residual: dihedral pdb=" CD ARG Q 216 " pdb=" NE ARG Q 216 " pdb=" CZ ARG Q 216 " pdb=" NH1 ARG Q 216 " ideal model delta sinusoidal sigma weight residual 0.00 76.32 -76.32 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CD ARG K 216 " pdb=" NE ARG K 216 " pdb=" CZ ARG K 216 " pdb=" NH1 ARG K 216 " ideal model delta sinusoidal sigma weight residual 0.00 -56.84 56.84 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" C ARG K 216 " pdb=" N ARG K 216 " pdb=" CA ARG K 216 " pdb=" CB ARG K 216 " ideal model delta harmonic sigma weight residual -122.60 -108.72 -13.88 0 2.50e+00 1.60e-01 3.08e+01 ... (remaining 19743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4065 0.054 - 0.108: 536 0.108 - 0.162: 27 0.162 - 0.216: 6 0.216 - 0.269: 1 Chirality restraints: 4635 Sorted by residual: chirality pdb=" CA ARG K 216 " pdb=" N ARG K 216 " pdb=" C ARG K 216 " pdb=" CB ARG K 216 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA PHE K 211 " pdb=" N PHE K 211 " pdb=" C PHE K 211 " pdb=" CB PHE K 211 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4632 not shown) Planarity restraints: 5985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 216 " -1.038 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG Q 216 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG Q 216 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 216 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 216 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 216 " 0.899 9.50e-02 1.11e+02 4.03e-01 9.85e+01 pdb=" NE ARG K 216 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG K 216 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 216 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 216 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 252 " -0.548 9.50e-02 1.11e+02 2.46e-01 3.69e+01 pdb=" NE ARG R 252 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG R 252 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG R 252 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 252 " -0.019 2.00e-02 2.50e+03 ... (remaining 5982 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3776 2.74 - 3.28: 33202 3.28 - 3.82: 53589 3.82 - 4.36: 53641 4.36 - 4.90: 91940 Nonbonded interactions: 236148 Sorted by model distance: nonbonded pdb=" OH TYR C 116 " pdb=" OXT ARG C 155 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR R 240 " pdb=" OE2 GLU R 298 " model vdw 2.214 3.040 nonbonded pdb=" O ASP L 95 " pdb=" OG1 THR L 99 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR M 240 " pdb=" OE2 GLU M 298 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR P 240 " pdb=" OE2 GLU P 298 " model vdw 2.222 3.040 ... (remaining 236143 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: 0.01 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' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.690 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.004 0.075 31860 Z= 0.201 Angle : 0.708 11.458 42867 Z= 0.391 Chirality : 0.035 0.269 4635 Planarity : 0.010 0.465 5985 Dihedral : 18.785 89.833 12150 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 0.37 % Allowed : 30.23 % Favored : 69.40 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 1.68 (0.14), residues: 4122 helix: 2.54 (0.10), residues: 2997 sheet: None (None), residues: 0 loop : -3.18 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 223 TYR 0.044 0.001 TYR B 116 PHE 0.044 0.002 PHE O 211 TRP 0.015 0.002 TRP A 77 HIS 0.004 0.001 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00405 (31860) covalent geometry : angle 0.70849 (42867) hydrogen bonds : bond 0.11242 ( 2290) hydrogen bonds : angle 4.61250 ( 6843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 425 time to evaluate : 0.813 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: R 90 MET cc_start: 0.8738 (mmt) cc_final: 0.8468 (mmm) REVERT: J 42 ARG cc_start: 0.7870 (ptp90) cc_final: 0.7661 (ptp90) REVERT: K 42 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7089 (mpt-90) REVERT: K 72 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8483 (tm-30) REVERT: K 215 GLN cc_start: 0.8294 (mt0) cc_final: 0.8047 (mt0) REVERT: L 42 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: L 90 MET cc_start: 0.9201 (mtp) cc_final: 0.8902 (mtp) REVERT: L 95 ASP cc_start: 0.8692 (t70) cc_final: 0.8214 (t70) REVERT: M 42 ARG cc_start: 0.8567 (ptm160) cc_final: 0.7880 (ptp-170) REVERT: O 221 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7845 (ttm110) REVERT: P 215 GLN cc_start: 0.8690 (tt0) cc_final: 0.8381 (tt0) REVERT: Q 260 MET cc_start: -0.2310 (mmp) cc_final: -0.2935 (tmm) REVERT: B 149 MET cc_start: 0.8008 (mmp) cc_final: 0.7133 (ptt) REVERT: C 33 MET cc_start: 0.0567 (ttp) cc_final: 0.0022 (ttp) REVERT: C 104 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 102 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7505 (ttm-80) REVERT: E 98 GLN cc_start: 0.8697 (tt0) cc_final: 0.8433 (tp40) REVERT: E 104 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8328 (tm-30) REVERT: E 149 MET cc_start: 0.8033 (mmp) cc_final: 0.7674 (tpt) REVERT: F 98 GLN cc_start: 0.8456 (tt0) cc_final: 0.8144 (tp40) REVERT: F 99 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7242 (ttt-90) REVERT: F 102 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8310 (ttp-110) REVERT: F 132 ARG cc_start: 0.7975 (tpt90) cc_final: 0.7669 (mmp80) REVERT: G 149 MET cc_start: 0.7449 (mmp) cc_final: 0.5955 (pmm) REVERT: H 95 ASN cc_start: 0.8973 (t0) cc_final: 0.8756 (t0) outliers start: 12 outliers final: 4 residues processed: 434 average time/residue: 0.1722 time to fit residues: 117.4506 Evaluate side-chains 415 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 411 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain H residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 238 GLN J 159 ASN K 238 GLN L 238 GLN N 238 GLN O 238 GLN P 238 GLN Q 238 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN H 41 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.210846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.117801 restraints weight = 49166.441| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.85 r_work: 0.3109 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31860 Z= 0.167 Angle : 0.537 6.669 42867 Z= 0.289 Chirality : 0.036 0.155 4635 Planarity : 0.004 0.173 5985 Dihedral : 3.693 49.222 4588 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 2.27 % Allowed : 28.31 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.15), residues: 4122 helix: 2.94 (0.10), residues: 2988 sheet: -2.52 (0.60), residues: 90 loop : -3.41 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 216 TYR 0.020 0.001 TYR B 116 PHE 0.030 0.001 PHE B 112 TRP 0.021 0.002 TRP F 77 HIS 0.001 0.000 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00352 (31860) covalent geometry : angle 0.53705 (42867) hydrogen bonds : bond 0.06586 ( 2290) hydrogen bonds : angle 3.70359 ( 6843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 423 time to evaluate : 0.888 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: R 101 ASP cc_start: 0.8797 (p0) cc_final: 0.8593 (p0) REVERT: J 324 MET cc_start: 0.8669 (mmm) cc_final: 0.8466 (mmp) REVERT: L 90 MET cc_start: 0.9263 (mtp) cc_final: 0.8978 (mtp) REVERT: L 95 ASP cc_start: 0.8807 (t70) cc_final: 0.8262 (t70) REVERT: M 202 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8270 (mmm) REVERT: N 159 ASN cc_start: 0.9265 (t0) cc_final: 0.8993 (t0) REVERT: O 221 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7892 (ttm110) REVERT: P 215 GLN cc_start: 0.8498 (tt0) cc_final: 0.8249 (tt0) REVERT: Q 42 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7832 (mtt-85) REVERT: Q 101 ASP cc_start: 0.8545 (p0) cc_final: 0.8301 (p0) REVERT: Q 221 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7599 (ttm110) REVERT: Q 260 MET cc_start: -0.2511 (mmp) cc_final: -0.3307 (tmm) REVERT: A 3 TYR cc_start: 0.1043 (OUTLIER) cc_final: -0.0068 (p90) REVERT: A 63 MET cc_start: 0.6845 (mpt) cc_final: 0.6442 (mpt) REVERT: B 99 ARG cc_start: 0.7110 (mmm-85) cc_final: 0.6598 (tpp-160) REVERT: B 148 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: C 33 MET cc_start: 0.1049 (ttp) cc_final: 0.0480 (ttp) REVERT: D 51 MET cc_start: 0.1826 (mmm) cc_final: 0.1431 (tpp) REVERT: E 98 GLN cc_start: 0.8332 (tt0) cc_final: 0.8125 (tp40) REVERT: F 98 GLN cc_start: 0.7974 (tt0) cc_final: 0.7639 (tp40) REVERT: F 99 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.6904 (ttt-90) REVERT: F 102 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8048 (ttp-110) REVERT: F 132 ARG cc_start: 0.8103 (tpt90) cc_final: 0.7690 (mmp80) REVERT: F 149 MET cc_start: 0.8792 (tpt) cc_final: 0.8157 (ptt) REVERT: H 111 GLN cc_start: 0.8882 (tp40) cc_final: 0.8546 (tp40) REVERT: H 149 MET cc_start: 0.8015 (ttp) cc_final: 0.7689 (ptt) outliers start: 73 outliers final: 40 residues processed: 469 average time/residue: 0.1684 time to fit residues: 124.3158 Evaluate side-chains 456 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 413 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 238 GLN Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 238 GLN Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 368 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 357 optimal weight: 0.8980 chunk 332 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 323 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 303 optimal weight: 0.3980 chunk 308 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 156 GLN K 159 ASN M 176 ASN P 156 GLN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN F 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.213019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118896 restraints weight = 49377.872| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.96 r_work: 0.3114 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31860 Z= 0.142 Angle : 0.509 7.336 42867 Z= 0.272 Chirality : 0.035 0.155 4635 Planarity : 0.003 0.124 5985 Dihedral : 3.610 50.250 4587 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 2.92 % Allowed : 27.84 % Favored : 69.24 % 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 aren not related in a simple way. whole: 2.12 (0.15), residues: 4122 helix: 3.01 (0.10), residues: 2979 sheet: -2.54 (0.60), residues: 90 loop : -3.39 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 221 TYR 0.018 0.001 TYR G 116 PHE 0.034 0.001 PHE O 211 TRP 0.013 0.002 TRP F 77 HIS 0.001 0.000 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00285 (31860) covalent geometry : angle 0.50862 (42867) hydrogen bonds : bond 0.06351 ( 2290) hydrogen bonds : angle 3.53784 ( 6843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 427 time to evaluate : 1.045 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: R 95 ASP cc_start: 0.8299 (t70) cc_final: 0.7990 (t70) REVERT: R 260 MET cc_start: -0.0370 (mmp) cc_final: -0.1355 (mmp) REVERT: J 126 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8090 (tm-30) REVERT: J 324 MET cc_start: 0.8740 (mmm) cc_final: 0.8530 (mmm) REVERT: K 36 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7412 (tt) REVERT: L 90 MET cc_start: 0.9291 (mtp) cc_final: 0.9019 (mtp) REVERT: L 95 ASP cc_start: 0.8782 (t70) cc_final: 0.8285 (t70) REVERT: M 202 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8321 (mmm) REVERT: N 56 GLU cc_start: 0.8914 (tp30) cc_final: 0.8661 (tp30) REVERT: N 159 ASN cc_start: 0.9263 (t0) cc_final: 0.8964 (t0) REVERT: O 221 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8033 (ttm110) REVERT: P 101 ASP cc_start: 0.8639 (p0) cc_final: 0.8376 (p0) REVERT: P 215 GLN cc_start: 0.8528 (tt0) cc_final: 0.8194 (tt0) REVERT: Q 185 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8083 (tm-30) REVERT: Q 221 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7654 (ttm110) REVERT: Q 260 MET cc_start: -0.2449 (mmp) cc_final: -0.3211 (tmm) REVERT: A 3 TYR cc_start: 0.1074 (OUTLIER) cc_final: 0.0044 (p90) REVERT: A 63 MET cc_start: 0.6519 (mpt) cc_final: 0.6159 (mpt) REVERT: B 99 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6610 (tpp-160) REVERT: B 148 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: C 1 MET cc_start: 0.3954 (pmm) cc_final: 0.1599 (tpt) REVERT: C 8 MET cc_start: 0.1164 (mmm) cc_final: 0.0790 (mtm) REVERT: C 33 MET cc_start: 0.1099 (ttp) cc_final: 0.0582 (ttp) REVERT: C 111 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: C 132 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7072 (mmm160) REVERT: D 51 MET cc_start: 0.2169 (mmm) cc_final: 0.1584 (tpp) REVERT: D 121 GLN cc_start: 0.7895 (tt0) cc_final: 0.7661 (tm-30) REVERT: F 98 GLN cc_start: 0.7881 (tt0) cc_final: 0.7543 (tp40) REVERT: F 99 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.6950 (ttt-90) REVERT: F 102 ARG cc_start: 0.8389 (ttm170) cc_final: 0.8048 (ttp-110) REVERT: F 132 ARG cc_start: 0.8105 (tpt90) cc_final: 0.7629 (mmp80) REVERT: F 149 MET cc_start: 0.8899 (tpt) cc_final: 0.8230 (ptt) outliers start: 94 outliers final: 53 residues processed: 489 average time/residue: 0.1965 time to fit residues: 149.5805 Evaluate side-chains 474 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 415 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 299 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 403 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN L 30 GLN M 176 ASN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN F 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.211192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117286 restraints weight = 49288.272| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.89 r_work: 0.3098 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31860 Z= 0.149 Angle : 0.512 9.570 42867 Z= 0.273 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.101 5985 Dihedral : 3.544 49.557 4585 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.36 % Favored : 93.45 % Rotamer: Outliers : 3.82 % Allowed : 26.66 % Favored : 69.52 % 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 aren not related in a simple way. whole: 2.17 (0.15), residues: 4122 helix: 3.06 (0.10), residues: 2979 sheet: -2.62 (0.59), residues: 90 loop : -3.40 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 109 TYR 0.015 0.001 TYR G 116 PHE 0.042 0.001 PHE O 211 TRP 0.012 0.002 TRP A 77 HIS 0.001 0.000 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00313 (31860) covalent geometry : angle 0.51229 (42867) hydrogen bonds : bond 0.06428 ( 2290) hydrogen bonds : angle 3.48247 ( 6843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 428 time to evaluate : 0.738 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: R 95 ASP cc_start: 0.8344 (t70) cc_final: 0.7936 (t70) REVERT: R 260 MET cc_start: -0.0602 (mmp) cc_final: -0.1254 (mmp) REVERT: J 126 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8109 (tm-30) REVERT: J 162 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8130 (mt-10) REVERT: J 217 ASP cc_start: 0.8627 (t0) cc_final: 0.8242 (t0) REVERT: J 324 MET cc_start: 0.8772 (mmm) cc_final: 0.8561 (mmm) REVERT: K 42 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7358 (mtm-85) REVERT: L 90 MET cc_start: 0.9328 (mtp) cc_final: 0.9063 (mtp) REVERT: L 95 ASP cc_start: 0.8758 (t70) cc_final: 0.8252 (t70) REVERT: N 56 GLU cc_start: 0.8874 (tp30) cc_final: 0.8651 (tp30) REVERT: N 159 ASN cc_start: 0.9277 (t0) cc_final: 0.8966 (t0) REVERT: O 36 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7067 (tt) REVERT: O 221 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8041 (ttm110) REVERT: P 101 ASP cc_start: 0.8711 (p0) cc_final: 0.8146 (p0) REVERT: P 215 GLN cc_start: 0.8569 (tt0) cc_final: 0.8253 (tt0) REVERT: P 260 MET cc_start: 0.2383 (pmm) cc_final: 0.1964 (ptp) REVERT: Q 42 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7792 (mtm-85) REVERT: Q 101 ASP cc_start: 0.8572 (p0) cc_final: 0.8347 (p0) REVERT: Q 185 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8096 (tm-30) REVERT: Q 214 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8186 (tt0) REVERT: Q 221 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7683 (ttm110) REVERT: Q 260 MET cc_start: -0.2445 (mmp) cc_final: -0.3213 (tmm) REVERT: A 3 TYR cc_start: 0.0911 (OUTLIER) cc_final: 0.0004 (p90) REVERT: A 114 MET cc_start: 0.8389 (tpt) cc_final: 0.8052 (tmm) REVERT: B 99 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6695 (tpp-160) REVERT: B 148 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: B 152 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7876 (p0) REVERT: C 1 MET cc_start: 0.4091 (pmm) cc_final: 0.2890 (ppp) REVERT: C 8 MET cc_start: 0.1179 (mmm) cc_final: 0.0799 (mtm) REVERT: C 33 MET cc_start: 0.1110 (ttp) cc_final: 0.0575 (ttp) REVERT: C 51 MET cc_start: 0.3389 (mmp) cc_final: 0.1376 (mtt) REVERT: C 111 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: C 132 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7072 (mmm160) REVERT: D 51 MET cc_start: 0.1797 (mmm) cc_final: 0.1262 (tpp) REVERT: D 121 GLN cc_start: 0.8043 (tt0) cc_final: 0.7838 (tm-30) REVERT: E 35 MET cc_start: -0.1574 (pmm) cc_final: -0.1871 (ptt) REVERT: E 149 MET cc_start: 0.7926 (mmp) cc_final: 0.7595 (tpt) REVERT: F 99 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6580 (ttt-90) REVERT: F 114 MET cc_start: 0.8625 (tmm) cc_final: 0.8414 (tmm) REVERT: F 132 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7629 (mmp80) REVERT: H 149 MET cc_start: 0.7940 (ttp) cc_final: 0.7704 (ptt) outliers start: 123 outliers final: 79 residues processed: 510 average time/residue: 0.1662 time to fit residues: 133.0160 Evaluate side-chains 504 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 419 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 401 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 284 optimal weight: 0.6980 chunk 353 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 176 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN E 111 GLN F 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.210896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117813 restraints weight = 48933.665| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.84 r_work: 0.3094 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31860 Z= 0.148 Angle : 0.518 9.985 42867 Z= 0.274 Chirality : 0.035 0.161 4635 Planarity : 0.004 0.137 5985 Dihedral : 3.548 48.202 4585 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.31 % Favored : 93.47 % Rotamer: Outliers : 3.57 % Allowed : 27.13 % Favored : 69.30 % 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 aren not related in a simple way. whole: 2.18 (0.15), residues: 4122 helix: 3.06 (0.10), residues: 2979 sheet: -2.65 (0.58), residues: 90 loop : -3.37 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 216 TYR 0.016 0.001 TYR G 116 PHE 0.045 0.001 PHE O 211 TRP 0.011 0.002 TRP B 77 HIS 0.001 0.000 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00310 (31860) covalent geometry : angle 0.51772 (42867) hydrogen bonds : bond 0.06412 ( 2290) hydrogen bonds : angle 3.45037 ( 6843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 423 time to evaluate : 1.006 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: R 95 ASP cc_start: 0.8268 (t70) cc_final: 0.7794 (t70) REVERT: R 260 MET cc_start: -0.0279 (mmp) cc_final: -0.0801 (mmp) REVERT: J 42 ARG cc_start: 0.7718 (ptp90) cc_final: 0.7479 (ptp90) REVERT: J 162 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8102 (mt-10) REVERT: J 217 ASP cc_start: 0.8672 (t0) cc_final: 0.8321 (t0) REVERT: K 36 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7413 (tt) REVERT: L 90 MET cc_start: 0.9345 (mtp) cc_final: 0.9099 (mtp) REVERT: L 126 GLU cc_start: 0.8971 (tt0) cc_final: 0.8668 (tm-30) REVERT: N 159 ASN cc_start: 0.9266 (t0) cc_final: 0.8954 (t0) REVERT: O 36 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7065 (tt) REVERT: O 42 ARG cc_start: 0.7735 (ptp90) cc_final: 0.7491 (ptp90) REVERT: O 159 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8634 (t0) REVERT: O 214 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7853 (mt-10) REVERT: O 221 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8061 (ttm110) REVERT: P 101 ASP cc_start: 0.8766 (p0) cc_final: 0.8292 (p0) REVERT: P 260 MET cc_start: 0.2534 (pmm) cc_final: 0.2199 (ptp) REVERT: Q 42 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7740 (mtt-85) REVERT: Q 101 ASP cc_start: 0.8639 (p0) cc_final: 0.8364 (p0) REVERT: Q 185 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8019 (tm-30) REVERT: Q 214 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8175 (tt0) REVERT: Q 221 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7690 (ttm110) REVERT: Q 260 MET cc_start: -0.2437 (mmp) cc_final: -0.3034 (tmm) REVERT: A 3 TYR cc_start: 0.0903 (OUTLIER) cc_final: -0.0011 (p90) REVERT: B 99 ARG cc_start: 0.7223 (mmm-85) cc_final: 0.6678 (tpp-160) REVERT: B 148 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: B 149 MET cc_start: 0.7896 (mmm) cc_final: 0.7355 (ptt) REVERT: C 1 MET cc_start: 0.3842 (pmm) cc_final: 0.2865 (ppp) REVERT: C 8 MET cc_start: 0.1176 (mmm) cc_final: 0.0799 (mtm) REVERT: C 51 MET cc_start: 0.3003 (mmp) cc_final: 0.1154 (mtt) REVERT: C 111 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: C 132 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7069 (mmm160) REVERT: D 51 MET cc_start: 0.1813 (mmm) cc_final: 0.1286 (tpp) REVERT: E 35 MET cc_start: -0.1756 (pmm) cc_final: -0.2016 (ptt) REVERT: E 149 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7557 (tpp) REVERT: F 99 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.6644 (ttt-90) REVERT: F 132 ARG cc_start: 0.8148 (tpt90) cc_final: 0.7624 (mmp80) REVERT: F 149 MET cc_start: 0.8672 (mmm) cc_final: 0.8060 (ppp) REVERT: H 149 MET cc_start: 0.8046 (ttp) cc_final: 0.7638 (ptt) outliers start: 115 outliers final: 82 residues processed: 501 average time/residue: 0.1789 time to fit residues: 141.0603 Evaluate side-chains 501 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 411 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 261 optimal weight: 0.8980 chunk 126 optimal weight: 0.3980 chunk 204 optimal weight: 0.0970 chunk 301 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 332 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 106 GLN K 159 ASN M 176 ASN D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.212088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118798 restraints weight = 49398.923| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.96 r_work: 0.3132 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31860 Z= 0.127 Angle : 0.503 8.956 42867 Z= 0.264 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.093 5985 Dihedral : 3.410 46.028 4583 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.87 % Favored : 93.91 % Rotamer: Outliers : 3.32 % Allowed : 27.34 % Favored : 69.34 % 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 aren not related in a simple way. whole: 2.40 (0.14), residues: 4122 helix: 3.18 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -3.12 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 109 TYR 0.013 0.001 TYR B 148 PHE 0.029 0.001 PHE O 211 TRP 0.009 0.001 TRP F 77 HIS 0.001 0.000 HIS R 198 Details of bonding type rmsd covalent geometry : bond 0.00246 (31860) covalent geometry : angle 0.50294 (42867) hydrogen bonds : bond 0.05964 ( 2290) hydrogen bonds : angle 3.31594 ( 6843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 427 time to evaluate : 0.767 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: R 94 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8797 (mp) REVERT: R 95 ASP cc_start: 0.8152 (t70) cc_final: 0.7576 (t70) REVERT: R 260 MET cc_start: -0.0473 (mmp) cc_final: -0.0928 (mmp) REVERT: J 42 ARG cc_start: 0.7651 (ptp90) cc_final: 0.7432 (ptp90) REVERT: J 162 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7979 (mt-10) REVERT: J 217 ASP cc_start: 0.8683 (t0) cc_final: 0.8345 (t0) REVERT: K 36 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7555 (tt) REVERT: K 78 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8866 (t0) REVERT: K 90 MET cc_start: 0.8466 (mtp) cc_final: 0.8210 (mtt) REVERT: K 159 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8759 (t0) REVERT: K 202 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: L 38 ASP cc_start: 0.8138 (p0) cc_final: 0.7384 (t70) REVERT: L 90 MET cc_start: 0.9281 (mtp) cc_final: 0.9057 (mtp) REVERT: L 92 MET cc_start: 0.9114 (tpp) cc_final: 0.8882 (mmm) REVERT: L 101 ASP cc_start: 0.8854 (p0) cc_final: 0.8488 (p0) REVERT: L 260 MET cc_start: 0.0653 (mmp) cc_final: -0.1797 (tmm) REVERT: M 126 GLU cc_start: 0.8968 (tt0) cc_final: 0.8704 (tm-30) REVERT: N 270 MET cc_start: 0.6158 (pmm) cc_final: 0.5933 (pmm) REVERT: O 36 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7007 (tt) REVERT: O 159 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8678 (t0) REVERT: O 214 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7865 (mt-10) REVERT: O 221 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8066 (ttm110) REVERT: P 101 ASP cc_start: 0.8778 (p0) cc_final: 0.8303 (p0) REVERT: P 188 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: P 260 MET cc_start: 0.2709 (OUTLIER) cc_final: 0.1131 (mmt) REVERT: Q 42 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7727 (mtm-85) REVERT: Q 101 ASP cc_start: 0.8699 (p0) cc_final: 0.8372 (p0) REVERT: Q 185 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8023 (tm-30) REVERT: Q 214 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8180 (tt0) REVERT: Q 221 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7630 (ttm110) REVERT: Q 260 MET cc_start: -0.2483 (mmp) cc_final: -0.3041 (tmm) REVERT: A 3 TYR cc_start: 0.1125 (OUTLIER) cc_final: 0.0040 (p90) REVERT: B 148 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: C 1 MET cc_start: 0.3731 (pmm) cc_final: 0.2828 (ppp) REVERT: C 8 MET cc_start: 0.1183 (mmm) cc_final: 0.0803 (mtm) REVERT: C 51 MET cc_start: 0.2746 (mmp) cc_final: 0.1008 (mtt) REVERT: C 111 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: C 132 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7082 (mmm160) REVERT: D 51 MET cc_start: 0.1916 (mmm) cc_final: 0.1364 (tpp) REVERT: D 121 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: E 35 MET cc_start: -0.1722 (pmm) cc_final: -0.2006 (ptt) REVERT: E 149 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7553 (tpp) REVERT: F 99 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.6701 (ttt-90) REVERT: F 132 ARG cc_start: 0.8144 (tpt90) cc_final: 0.7615 (mmp80) REVERT: F 149 MET cc_start: 0.8690 (mmm) cc_final: 0.8051 (ppp) REVERT: I 114 MET cc_start: 0.8762 (tpp) cc_final: 0.8526 (ttm) outliers start: 107 outliers final: 66 residues processed: 496 average time/residue: 0.1571 time to fit residues: 123.9282 Evaluate side-chains 487 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 406 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 260 MET Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 318 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 314 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 313 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 367 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN M 171 GLN ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN F 111 GLN I 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.212247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119818 restraints weight = 48904.670| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.86 r_work: 0.3128 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31860 Z= 0.132 Angle : 0.518 11.304 42867 Z= 0.271 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.082 5985 Dihedral : 3.380 45.788 4581 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 3.57 % Allowed : 27.44 % Favored : 68.99 % 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 aren not related in a simple way. whole: 2.39 (0.14), residues: 4122 helix: 3.15 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.08 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.011 0.001 TYR B 148 PHE 0.028 0.001 PHE A 112 TRP 0.009 0.001 TRP B 77 HIS 0.000 0.000 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00267 (31860) covalent geometry : angle 0.51808 (42867) hydrogen bonds : bond 0.06008 ( 2290) hydrogen bonds : angle 3.31366 ( 6843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 419 time to evaluate : 0.993 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: R 94 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8775 (mp) REVERT: R 95 ASP cc_start: 0.8205 (t70) cc_final: 0.7589 (t70) REVERT: R 260 MET cc_start: -0.0156 (mmp) cc_final: -0.0618 (mmp) REVERT: J 42 ARG cc_start: 0.7637 (ptp90) cc_final: 0.7384 (ptp90) REVERT: J 162 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7932 (mt-10) REVERT: J 217 ASP cc_start: 0.8576 (t0) cc_final: 0.8212 (t0) REVERT: K 36 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7461 (tt) REVERT: K 78 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8852 (t0) REVERT: K 90 MET cc_start: 0.8425 (mtp) cc_final: 0.8172 (mtt) REVERT: K 202 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8104 (mmm) REVERT: L 38 ASP cc_start: 0.8085 (p0) cc_final: 0.7394 (t70) REVERT: L 90 MET cc_start: 0.9311 (mtp) cc_final: 0.9070 (mtp) REVERT: L 101 ASP cc_start: 0.8838 (p0) cc_final: 0.8417 (p0) REVERT: L 260 MET cc_start: 0.0323 (mmp) cc_final: -0.1978 (tmm) REVERT: N 228 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7453 (pp) REVERT: O 36 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7010 (tt) REVERT: O 159 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8697 (t0) REVERT: O 214 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7874 (mt-10) REVERT: O 221 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8056 (ttm110) REVERT: P 101 ASP cc_start: 0.8829 (p0) cc_final: 0.8375 (p0) REVERT: P 188 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: P 260 MET cc_start: 0.2544 (OUTLIER) cc_final: 0.1138 (mmt) REVERT: Q 42 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7742 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8870 (tp30) cc_final: 0.8614 (tp30) REVERT: Q 101 ASP cc_start: 0.8656 (p0) cc_final: 0.8356 (p0) REVERT: Q 185 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7988 (tm-30) REVERT: Q 214 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8188 (tt0) REVERT: Q 221 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7622 (ttm110) REVERT: Q 260 MET cc_start: -0.2487 (mmp) cc_final: -0.3044 (tmm) REVERT: A 3 TYR cc_start: 0.1132 (OUTLIER) cc_final: 0.0053 (p90) REVERT: B 148 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: B 149 MET cc_start: 0.7916 (mmm) cc_final: 0.7198 (ptt) REVERT: C 1 MET cc_start: 0.3901 (pmm) cc_final: 0.3036 (ppp) REVERT: C 8 MET cc_start: 0.1185 (mmm) cc_final: 0.0806 (mtm) REVERT: C 51 MET cc_start: 0.2736 (mmp) cc_final: 0.1004 (mtt) REVERT: C 111 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: D 51 MET cc_start: 0.1864 (mmm) cc_final: 0.1305 (tpp) REVERT: D 121 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: E 35 MET cc_start: -0.1725 (pmm) cc_final: -0.2006 (ptt) REVERT: E 99 ARG cc_start: 0.7254 (mmm-85) cc_final: 0.6400 (ttt-90) REVERT: E 109 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7443 (tpp80) REVERT: E 132 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7482 (mmp80) REVERT: E 149 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7558 (tpp) REVERT: E 155 ARG cc_start: 0.6495 (ttp80) cc_final: 0.6196 (tmm-80) REVERT: F 99 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6692 (ttt-90) REVERT: F 109 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7166 (tpp80) REVERT: F 132 ARG cc_start: 0.8149 (tpt90) cc_final: 0.7613 (mmp80) REVERT: H 149 MET cc_start: 0.8027 (ttp) cc_final: 0.7684 (ptt) REVERT: I 114 MET cc_start: 0.8755 (tpp) cc_final: 0.8543 (ttm) outliers start: 115 outliers final: 84 residues processed: 493 average time/residue: 0.1682 time to fit residues: 131.7497 Evaluate side-chains 516 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 418 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 260 MET Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 209 optimal weight: 0.0970 chunk 357 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 374 optimal weight: 6.9990 chunk 379 optimal weight: 30.0000 chunk 97 optimal weight: 0.0570 chunk 85 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.9098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN M 171 GLN Q 30 GLN A 121 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.210390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116268 restraints weight = 48688.918| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.87 r_work: 0.3084 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31860 Z= 0.158 Angle : 0.543 10.087 42867 Z= 0.285 Chirality : 0.035 0.162 4635 Planarity : 0.003 0.082 5985 Dihedral : 3.460 45.299 4581 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 3.51 % Allowed : 27.62 % Favored : 68.87 % 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 aren not related in a simple way. whole: 2.32 (0.14), residues: 4122 helix: 3.09 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.09 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 216 TYR 0.010 0.001 TYR B 148 PHE 0.027 0.001 PHE A 112 TRP 0.014 0.002 TRP E 77 HIS 0.001 0.000 HIS Q 198 Details of bonding type rmsd covalent geometry : bond 0.00342 (31860) covalent geometry : angle 0.54259 (42867) hydrogen bonds : bond 0.06482 ( 2290) hydrogen bonds : angle 3.40946 ( 6843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 428 time to evaluate : 1.089 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: R 126 GLU cc_start: 0.8926 (tt0) cc_final: 0.8650 (tm-30) REVERT: R 260 MET cc_start: 0.0226 (mmp) cc_final: -0.0414 (mmp) REVERT: J 42 ARG cc_start: 0.7662 (ptp90) cc_final: 0.7440 (ptp90) REVERT: J 90 MET cc_start: 0.9105 (ttm) cc_final: 0.8727 (ttt) REVERT: J 101 ASP cc_start: 0.8819 (p0) cc_final: 0.8611 (p0) REVERT: J 162 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8004 (mt-10) REVERT: J 217 ASP cc_start: 0.8663 (t0) cc_final: 0.8342 (t0) REVERT: K 36 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7395 (tt) REVERT: K 78 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8882 (t0) REVERT: K 90 MET cc_start: 0.8495 (mtp) cc_final: 0.8213 (mtt) REVERT: K 202 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: K 221 ARG cc_start: 0.8527 (tpp80) cc_final: 0.8183 (tpp80) REVERT: L 38 ASP cc_start: 0.7944 (p0) cc_final: 0.7384 (t70) REVERT: L 90 MET cc_start: 0.9392 (mtp) cc_final: 0.9120 (mtp) REVERT: L 126 GLU cc_start: 0.8972 (tt0) cc_final: 0.8689 (tm-30) REVERT: L 260 MET cc_start: 0.0208 (mmp) cc_final: -0.2048 (tmm) REVERT: N 101 ASP cc_start: 0.8678 (p0) cc_final: 0.8093 (p0) REVERT: N 126 GLU cc_start: 0.8790 (tt0) cc_final: 0.8481 (tm-30) REVERT: N 159 ASN cc_start: 0.9315 (t0) cc_final: 0.9052 (t0) REVERT: O 36 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7126 (tt) REVERT: O 159 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8693 (t0) REVERT: O 214 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7902 (mt-10) REVERT: O 221 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8122 (ttm110) REVERT: P 101 ASP cc_start: 0.8819 (p0) cc_final: 0.8353 (p0) REVERT: P 188 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: Q 56 GLU cc_start: 0.8858 (tp30) cc_final: 0.8580 (tp30) REVERT: Q 101 ASP cc_start: 0.8650 (p0) cc_final: 0.8404 (p0) REVERT: Q 185 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8061 (tm-30) REVERT: Q 214 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8195 (tt0) REVERT: Q 221 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7711 (ttm110) REVERT: Q 260 MET cc_start: -0.2430 (mmp) cc_final: -0.2994 (tmm) REVERT: A 3 TYR cc_start: 0.1326 (OUTLIER) cc_final: 0.0273 (p90) REVERT: B 99 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6659 (tpp-160) REVERT: B 148 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: C 1 MET cc_start: 0.3942 (pmm) cc_final: 0.3018 (ppp) REVERT: C 8 MET cc_start: 0.1138 (mmm) cc_final: 0.0751 (mtm) REVERT: C 51 MET cc_start: 0.2956 (mmp) cc_final: 0.1215 (mtt) REVERT: C 111 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: D 51 MET cc_start: 0.1985 (mmm) cc_final: 0.1444 (tpp) REVERT: D 111 GLN cc_start: 0.8625 (pp30) cc_final: 0.8277 (pt0) REVERT: D 121 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: E 35 MET cc_start: -0.1717 (pmm) cc_final: -0.1998 (ptt) REVERT: E 99 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.6410 (ttt-90) REVERT: E 109 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7519 (tpp80) REVERT: E 132 ARG cc_start: 0.7876 (tpt90) cc_final: 0.7481 (mmp80) REVERT: E 149 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7550 (tpp) REVERT: E 155 ARG cc_start: 0.6352 (ttp80) cc_final: 0.6129 (ttp80) REVERT: F 99 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.6590 (ttt-90) REVERT: F 132 ARG cc_start: 0.8095 (tpt90) cc_final: 0.7541 (mmp80) REVERT: F 149 MET cc_start: 0.8709 (mmm) cc_final: 0.7840 (ptp) REVERT: H 149 MET cc_start: 0.8051 (ttp) cc_final: 0.7689 (ptt) REVERT: I 148 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8311 (m-10) outliers start: 113 outliers final: 89 residues processed: 504 average time/residue: 0.1847 time to fit residues: 145.6938 Evaluate side-chains 525 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 424 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 33 optimal weight: 0.9980 chunk 317 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 171 GLN M 176 ASN D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.210798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117060 restraints weight = 49486.590| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.88 r_work: 0.3108 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31860 Z= 0.138 Angle : 0.539 11.740 42867 Z= 0.280 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.074 5985 Dihedral : 3.413 43.370 4581 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 3.26 % Allowed : 28.27 % Favored : 68.47 % 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 aren not related in a simple way. whole: 2.36 (0.14), residues: 4122 helix: 3.12 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.06 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 221 TYR 0.011 0.001 TYR B 148 PHE 0.025 0.001 PHE G 112 TRP 0.010 0.002 TRP B 77 HIS 0.001 0.000 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00283 (31860) covalent geometry : angle 0.53877 (42867) hydrogen bonds : bond 0.06170 ( 2290) hydrogen bonds : angle 3.34270 ( 6843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 430 time to evaluate : 1.084 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: R 95 ASP cc_start: 0.8205 (t70) cc_final: 0.7646 (t70) REVERT: R 126 GLU cc_start: 0.8938 (tt0) cc_final: 0.8603 (tm-30) REVERT: R 260 MET cc_start: 0.0225 (mmp) cc_final: -0.0408 (mmp) REVERT: J 90 MET cc_start: 0.9093 (ttm) cc_final: 0.8714 (ttm) REVERT: J 162 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7941 (mt-10) REVERT: J 217 ASP cc_start: 0.8658 (t0) cc_final: 0.8338 (t0) REVERT: K 36 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7393 (tt) REVERT: K 78 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (t0) REVERT: K 90 MET cc_start: 0.8437 (mtp) cc_final: 0.8185 (mtt) REVERT: K 202 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8124 (mmm) REVERT: K 221 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8246 (tpp80) REVERT: L 38 ASP cc_start: 0.7912 (p0) cc_final: 0.7390 (t70) REVERT: L 90 MET cc_start: 0.9345 (mtp) cc_final: 0.9122 (mtp) REVERT: L 101 ASP cc_start: 0.8838 (p0) cc_final: 0.8456 (p0) REVERT: L 124 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8750 (mt0) REVERT: L 126 GLU cc_start: 0.8966 (tt0) cc_final: 0.8689 (tm-30) REVERT: N 159 ASN cc_start: 0.9247 (t0) cc_final: 0.8985 (t0) REVERT: N 214 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8015 (mt-10) REVERT: O 36 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7109 (tt) REVERT: O 159 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8669 (t0) REVERT: O 211 PHE cc_start: 0.7307 (m-80) cc_final: 0.6950 (t80) REVERT: O 214 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7904 (mt-10) REVERT: O 221 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8161 (ttm110) REVERT: P 101 ASP cc_start: 0.8788 (p0) cc_final: 0.8347 (p0) REVERT: P 188 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7978 (mm-40) REVERT: P 260 MET cc_start: 0.2919 (pmm) cc_final: 0.1786 (mmt) REVERT: Q 42 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7670 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8855 (tp30) cc_final: 0.8607 (tp30) REVERT: Q 101 ASP cc_start: 0.8747 (p0) cc_final: 0.8461 (p0) REVERT: Q 185 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8047 (tm-30) REVERT: Q 214 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8195 (tt0) REVERT: Q 221 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7697 (ttm110) REVERT: Q 260 MET cc_start: -0.2465 (mmp) cc_final: -0.3018 (tmm) REVERT: A 3 TYR cc_start: 0.1332 (OUTLIER) cc_final: 0.0268 (p90) REVERT: A 149 MET cc_start: 0.8660 (tpp) cc_final: 0.8090 (ppp) REVERT: B 99 ARG cc_start: 0.7215 (mmm-85) cc_final: 0.6685 (tpp-160) REVERT: B 148 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: C 1 MET cc_start: 0.4087 (pmm) cc_final: 0.3135 (ppp) REVERT: C 8 MET cc_start: 0.1140 (mmm) cc_final: 0.0753 (mtm) REVERT: C 51 MET cc_start: 0.2771 (mmp) cc_final: 0.1053 (mtt) REVERT: C 111 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: D 51 MET cc_start: 0.2092 (mmm) cc_final: 0.1563 (tpp) REVERT: D 111 GLN cc_start: 0.8644 (pp30) cc_final: 0.8301 (pt0) REVERT: E 35 MET cc_start: -0.1715 (pmm) cc_final: -0.2071 (ptt) REVERT: E 99 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6406 (ttt-90) REVERT: E 109 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7465 (tpp80) REVERT: E 132 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7513 (mmp80) REVERT: E 149 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7501 (tpp) REVERT: E 155 ARG cc_start: 0.6328 (ttp80) cc_final: 0.6108 (ttp80) REVERT: F 99 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6565 (ttt-90) REVERT: F 132 ARG cc_start: 0.8143 (tpt90) cc_final: 0.7608 (mmp80) REVERT: H 149 MET cc_start: 0.8046 (ttp) cc_final: 0.7675 (ptt) REVERT: I 148 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8284 (m-10) outliers start: 105 outliers final: 80 residues processed: 497 average time/residue: 0.1971 time to fit residues: 152.9621 Evaluate side-chains 514 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 422 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 399 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 337 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 317 optimal weight: 0.0970 chunk 202 optimal weight: 8.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 171 GLN D 121 GLN F 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.211496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117670 restraints weight = 49165.037| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.97 r_work: 0.3099 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31860 Z= 0.139 Angle : 0.545 10.324 42867 Z= 0.284 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.073 5985 Dihedral : 3.398 42.489 4581 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 3.13 % Allowed : 28.31 % Favored : 68.56 % 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 aren not related in a simple way. whole: 2.37 (0.14), residues: 4122 helix: 3.12 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.04 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 221 TYR 0.010 0.001 TYR B 148 PHE 0.028 0.001 PHE A 112 TRP 0.010 0.001 TRP A 77 HIS 0.001 0.000 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00288 (31860) covalent geometry : angle 0.54496 (42867) hydrogen bonds : bond 0.06153 ( 2290) hydrogen bonds : angle 3.33307 ( 6843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 427 time to evaluate : 1.205 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: R 95 ASP cc_start: 0.8236 (t70) cc_final: 0.7675 (t70) REVERT: R 126 GLU cc_start: 0.8939 (tt0) cc_final: 0.8607 (tm-30) REVERT: R 260 MET cc_start: -0.0075 (mmp) cc_final: -0.0756 (mmp) REVERT: J 90 MET cc_start: 0.9074 (ttm) cc_final: 0.8707 (ttm) REVERT: J 162 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7999 (mt-10) REVERT: J 217 ASP cc_start: 0.8660 (t0) cc_final: 0.8350 (t0) REVERT: K 36 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7420 (tt) REVERT: K 42 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.6992 (mtm-85) REVERT: K 78 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8868 (t0) REVERT: K 90 MET cc_start: 0.8437 (mtp) cc_final: 0.8188 (mtt) REVERT: K 159 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8765 (t0) REVERT: K 202 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: K 221 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8319 (tpp80) REVERT: L 38 ASP cc_start: 0.7906 (p0) cc_final: 0.7396 (t70) REVERT: L 90 MET cc_start: 0.9340 (mtp) cc_final: 0.9113 (mtp) REVERT: L 101 ASP cc_start: 0.8836 (p0) cc_final: 0.8438 (p0) REVERT: L 124 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8755 (mt0) REVERT: L 126 GLU cc_start: 0.8978 (tt0) cc_final: 0.8685 (tm-30) REVERT: N 159 ASN cc_start: 0.9272 (t0) cc_final: 0.9004 (t0) REVERT: N 214 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8015 (mt-10) REVERT: O 36 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7113 (tt) REVERT: O 159 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8677 (t0) REVERT: O 207 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8653 (tp30) REVERT: O 211 PHE cc_start: 0.7275 (m-80) cc_final: 0.7004 (t80) REVERT: O 214 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7943 (mt-10) REVERT: O 221 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8184 (ttm110) REVERT: P 101 ASP cc_start: 0.8813 (p0) cc_final: 0.8372 (p0) REVERT: P 126 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: P 188 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7981 (mm-40) REVERT: P 260 MET cc_start: 0.2965 (pmm) cc_final: 0.1972 (mmt) REVERT: Q 42 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7683 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8858 (tp30) cc_final: 0.8600 (tp30) REVERT: Q 101 ASP cc_start: 0.8781 (p0) cc_final: 0.8502 (p0) REVERT: Q 185 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8010 (tm-30) REVERT: Q 214 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8195 (tt0) REVERT: Q 221 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7686 (ttm110) REVERT: Q 260 MET cc_start: -0.2486 (mmp) cc_final: -0.3041 (tmm) REVERT: A 3 TYR cc_start: 0.1320 (OUTLIER) cc_final: 0.0279 (p90) REVERT: A 149 MET cc_start: 0.8643 (tpp) cc_final: 0.8079 (ppp) REVERT: B 99 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6603 (tpp-160) REVERT: B 148 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: C 1 MET cc_start: 0.4037 (pmm) cc_final: 0.3204 (ppp) REVERT: C 8 MET cc_start: 0.1131 (mmm) cc_final: 0.0753 (mtm) REVERT: C 51 MET cc_start: 0.2924 (mmp) cc_final: 0.1100 (mtt) REVERT: C 111 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: D 51 MET cc_start: 0.2076 (mmm) cc_final: 0.1548 (tpp) REVERT: D 111 GLN cc_start: 0.8634 (pp30) cc_final: 0.8278 (pt0) REVERT: E 35 MET cc_start: -0.1857 (pmm) cc_final: -0.2187 (ptt) REVERT: E 99 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6395 (ttt-90) REVERT: E 109 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7442 (tpp80) REVERT: E 132 ARG cc_start: 0.7871 (tpt90) cc_final: 0.7479 (mmp80) REVERT: F 99 ARG cc_start: 0.7420 (mmm-85) cc_final: 0.6610 (ttt-90) REVERT: F 132 ARG cc_start: 0.8136 (tpt90) cc_final: 0.7603 (mmp80) REVERT: H 149 MET cc_start: 0.8005 (ttp) cc_final: 0.7651 (ptt) REVERT: I 148 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8316 (m-10) outliers start: 101 outliers final: 85 residues processed: 492 average time/residue: 0.2007 time to fit residues: 153.8078 Evaluate side-chains 518 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 420 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 40 ILE Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 31 optimal weight: 0.6980 chunk 348 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 315 optimal weight: 10.0000 chunk 271 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 171 GLN D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.216022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121605 restraints weight = 49172.768| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.02 r_work: 0.3106 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31860 Z= 0.137 Angle : 0.548 10.335 42867 Z= 0.285 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.070 5985 Dihedral : 3.394 41.932 4581 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 3.38 % Allowed : 28.06 % Favored : 68.56 % 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 aren not related in a simple way. whole: 2.39 (0.14), residues: 4122 helix: 3.13 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.03 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 42 TYR 0.010 0.001 TYR L 62 PHE 0.025 0.001 PHE A 112 TRP 0.009 0.001 TRP A 77 HIS 0.000 0.000 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00281 (31860) covalent geometry : angle 0.54800 (42867) hydrogen bonds : bond 0.06108 ( 2290) hydrogen bonds : angle 3.31090 ( 6843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9419.35 seconds wall clock time: 160 minutes 55.05 seconds (9655.05 seconds total)